4V4N | pdb_00004v4n

Structure of the Methanococcus jannaschii ribosome-SecYEBeta channel complex


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
B [auth A8]SCOP2B SuperfamilySec-beta subunit 8040632 3000289 SCOP2B (2022-06-29)
I [auth AX]SCOP2B SuperfamilySecY-like 8040629 3000333 SCOP2B (2022-06-29)
A [auth A7]SCOP2B SuperfamilyProtein translocase subunit SecE-like 8040630 3002174 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
B [auth A8]Ribosomal_S4ee4v4nA81 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_S4eECOD (v295)
C [auth Af]Ribosomal_S4ee4v4nAf1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_S4eECOD (v295)
D [auth AQ]Ribosomal_S4ee4v4nAQ1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_S4eECOD (v295)
E [auth AS]Ribosomal_S4ee4v4nAS1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_S4eECOD (v295)
F [auth AT]Ribosomal_S4ee4v4nAT1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_S4eECOD (v295)
G [auth AU]Ribosomal_S4ee4v4nAU1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_S4eECOD (v295)
H [auth AW]Ribosomal_S4ee4v4nAW1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_S4eECOD (v295)
I [auth AX]Ribosomal_S4ee4v4nAX1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_S4eECOD (v295)
L [auth B3]Ribosomal_S4ee4v4nB31 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_S4eECOD (v295)
YA [auth AG]Ribosomal_S4ee4v4nAG1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_S4eECOD (v295)
M [auth BA]Ribosomal_S4ee4v4nBA1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_S4eECOD (v295)
N [auth BB]FlaF_Ig-likee4v4nBB1 A: alpha arraysX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: FlaF_Ig-likeECOD (v295)
O [auth BC]Ribosomal_S4ee4v4nBC1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_S4eECOD (v295)
P [auth BD]KAsynt_C_assoce4v4nBD1 A: alpha arraysX: Type II ABC importer transmembrane domain foldH: Type II ABC importer transmembrane domain foldT: Type II ABC importer transmembrane domain foldF: KAsynt_C_assocECOD (v295)
Q [auth BE]Ribosomal_S4ee4v4nBE1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_S4eECOD (v295)
Q [auth BE]Ribosomal_L13e4v4nBE3 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
R [auth BF]KAsynt_C_assoce4v4nBF2 A: alpha arraysX: Type II ABC importer transmembrane domain foldH: Type II ABC importer transmembrane domain foldT: Type II ABC importer transmembrane domain foldF: KAsynt_C_assocECOD (v295)
R [auth BF]AAA_16e4v4nBF3 A: alpha arraysX: Trefoil/Plexin domain-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: AAA_16ECOD (v295)
S [auth BG]Ribosomal_L13e4v4nBG1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
T [auth BH]Ribosomal_L13e4v4nBH1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
V [auth BJ]Ribosomal_L13e4v4nBJ1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
W [auth BK]Ribosomal_S17,Ribosomal_S17_Ne4v4nBK1 A: alpha arraysX: OB-foldH: Nucleic acid-binding proteinT: Nucleic acid-binding proteinF: Ribosomal_S17,Ribosomal_S17_NECOD (v295)
Y [auth BM]Ribosomal_L13e4v4nBM1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
Z [auth BN]Ribosomal_L13e4v4nBN1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
AA [auth BO]Cellulasee4v4nBO1 A: alpha arraysX: HAD domain-likeH: HAD domain-relatedT: PIN domain-likeF: CellulaseECOD (v295)
BA [auth BP]Ribosomal_L13e4v4nBP1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
CA [auth BQ]Ribosomal_L13e4v4nBQ1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
DA [auth BR]Cellulasee4v4nBR1 A: alpha arraysX: HAD domain-likeH: HAD domain-relatedT: PIN domain-likeF: CellulaseECOD (v295)
EA [auth BS]Ribosomal_L13e4v4nBS1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
FA [auth BT]Cellulasee4v4nBT1 A: alpha arraysX: HAD domain-likeH: HAD domain-relatedT: PIN domain-likeF: CellulaseECOD (v295)
GA [auth BU]Ribosomal_L13e4v4nBU1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
HA [auth BV]Ribosomal_L13e4v4nBV1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
JA [auth BX]Ribosomal_L13e4v4nBX1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
KA [auth BY]Ribosomal_L13e4v4nBY1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
GB [auth AK]Ribosomal_L13e4v4nAK1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
NA [auth A5]Ribosomal_L13e4v4nA51 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
OA [auth AA]Ribosomal_L13e4v4nAA1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
PA [auth Aa]Ribosomal_L13e4v4nAa1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
QA [auth AB]Ribosomal_L13e4v4nAB1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
RA [auth Ab]Ribosomal_L13e4v4nAb1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
SA [auth AC]Ribosomal_L13e4v4nAC1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
SA [auth AC]Ribosomal_S18e4v4nAC2 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF: Ribosomal_S18ECOD (v295)
TA [auth AD]Ribosomal_L13e4v4nAD1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
UA [auth Ad]V_ATPase_Ie4v4nAd1 A: alpha arraysX: Alpha-beta plaitsH: Pseudouridine synthaseT: Pseudouridine synthaseF: V_ATPase_IECOD (v295)
VA [auth AE]Ribosomal_L13e4v4nAE1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
WA [auth Ae]Ribosomal_L13e4v4nAe1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
XA [auth AF]Ribosomal_L13e4v4nAF1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
ZA [auth Ag]Ribosomal_L13e4v4nAg1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
AB [auth AH]Ribosomal_L13e4v4nAH1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
CB [auth AI]Ribosomal_L13e4v4nAI1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
DB [auth Ai]Ribosomal_L5ee4v4nAi1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L5eECOD (v295)
FB [auth Aj]Ribosomal_L5ee4v4nAj1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L5eECOD (v295)
HB [auth Ak]Ribosomal_L5ee4v4nAk1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L5eECOD (v295)
IB [auth AL]Ribosomal_L5ee4v4nAL1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L5eECOD (v295)
JB [auth AM]Ribosomal_L5ee4v4nAM1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L5eECOD (v295)
KB [auth AN]PemK_toxine4v4nAN1 A: alpha arraysX: SH3H: SH3T: SH3F: PemK_toxinECOD (v295)
LB [auth AO]Ribosomal_L5ee4v4nAO1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L5eECOD (v295)
MB [auth AP]Ribosomal_L27e4v4nAP1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L27ECOD (v295)
NB [auth AR]Ribosomal_L27e4v4nAR1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L27ECOD (v295)
OB [auth AV]Ribosomal_L27e4v4nAV1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L27ECOD (v295)
PB [auth AY]Ribosomal_L27e4v4nAY1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L27ECOD (v295)
QB [auth AZ]Ribosomal_L27e4v4nAZ1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L27ECOD (v295)
EB [auth AJ]Ribosomal_L5ee4v4nAJ1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L5eECOD (v295)
IA [auth BW]Ribosomal_L13e4v4nBW1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
X [auth BL]Ribosomal_L13e4v4nBL1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
U [auth BI]Ribosomal_L13e4v4nBI1 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_L13ECOD (v295)
A [auth A7]Ribosomal_S4ee4v4nA71 A: alpha arraysX: VP4 membrane interaction domainH: VP4 membrane interaction domainT: VP4 membrane interaction domainF: Ribosomal_S4eECOD (v295)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
I [auth AX]PF10559Plug domain of Sec61p (Plug_translocon)Plug domain of Sec61pThe Sec61/SecY translocon mediates translocation of proteins across the membrane and integration of membrane proteins into the lipid bilayer. The structure of the translocon revealed a plug domain blocking the pore on the lumenal side.The plug is unl ...The Sec61/SecY translocon mediates translocation of proteins across the membrane and integration of membrane proteins into the lipid bilayer. The structure of the translocon revealed a plug domain blocking the pore on the lumenal side.The plug is unlikely to be important for sealing the translocation pore in yeast but it plays a role in stabilising Sec61p during translocon formation. The domain runs from residues 52-74 [1].
Domain
I [auth AX]PF00344SecY (SecY)SecY- Family
A [auth A7]PF00584SecE/Sec61-gamma subunits of protein translocation complex (SecE)SecE/Sec61-gamma subunits of protein translocation complex- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
B [auth A8]Preprotein translocase subunit SecG-
C [auth Af]50S ribosomal protein L39E---
D [auth AQ]50S ribosomal protein L19E---
E [auth AS]50S ribosomal protein L22P---
F [auth AT]50S ribosomal protein L23P---
G [auth AU]50S ribosomal protein L24P---
H [auth AW]50S ribosomal protein L29P---
I [auth AX]Protein translocase subunit SecY
J [auth B1]E-tRNA---
K [auth B2]16S ribosomal RNA---
L [auth B3],
YA [auth AG]
30S ribosomal protein L7AE---
M [auth BA]30S ribosomal protein S3AE---
N [auth BB]30S ribosomal protein S2P---
O [auth BC]30S ribosomal protein S3P---
P [auth BD]30S ribosomal protein S4P---
Q [auth BE]30S ribosomal protein S4E---
R [auth BF]30S ribosomal protein S5P---
S [auth BG]30S ribosomal protein S6E---
T [auth BH]30S ribosomal protein S7P---
V [auth BJ]30S ribosomal protein S8E---
W [auth BK]30S ribosomal protein S9P---
Y [auth BM]30S ribosomal protein S11P---
Z [auth BN]30S ribosomal protein S12P---
AA [auth BO]30S ribosomal protein S13P---
BA [auth BP]30S ribosomal protein S14P---
CA [auth BQ]30S ribosomal protein S15P/S13E---
DA [auth BR]30S ribosomal protein S17P---
EA [auth BS]30S ribosomal protein S17E---
FA [auth BT]30S ribosomal protein S19P---
GA [auth BU]30S ribosomal protein S19E---
HA [auth BV]30S ribosomal protein S24E---
JA [auth BX]30S ribosomal protein S28E---
KA [auth BY]30S ribosomal protein S27AE---
LA [auth A1]23S ribosomal RNA---
MA [auth A3]5S ribosomal RNA---
GB [auth AK],
NA [auth A5]
50S ribosomal protein L14E---
OA [auth AA]50S ribosomal protein L1P---
PA [auth Aa]50S ribosomal protein L31E---
QA [auth AB]50S ribosomal protein L2---
RA [auth Ab]50S ribosomal protein L32E---
SA [auth AC]50S ribosomal protein L3P---
TA [auth AD]50S ribosomal protein L4P---
UA [auth Ad]50S ribosomal protein L34E---
VA [auth AE]50S ribosomal protein L5P---
WA [auth Ae]50S ribosomal protein L37E---
XA [auth AF]50S ribosomal protein L6P---
ZA [auth Ag]50S ribosomal protein L40E---
AB [auth AH]50S ribosomal protein L11P---
BB [auth Ah]50S ribosomal protein L41E---
CB [auth AI]50S ribosomal protein L13P---
DB [auth Ai]50S ribosomal protein L37AE---
FB [auth Aj]50S ribosomal protein L44E---
HB [auth Ak]50S ribosomal protein P0/L10E---
IB [auth AL]50S ribosomal protein L15P---
JB [auth AM]50S ribosomal protein L15E---
KB [auth AN]50S ribosomal protein L10E/L16---
LB [auth AO]50S ribosomal protein L18P---
MB [auth AP]50S ribosomal protein L18E---
NB [auth AR]50S ribosomal protein L21E---
OB [auth AV]50S ribosomal protein L24E---
PB [auth AY]50S ribosomal protein L30P---
QB [auth AZ]50S ribosomal protein L30E---
EB [auth AJ]50S ribosomal protein L14P---
IA [auth BW]30S ribosomal protein S27E---
X [auth BL]30S ribosomal protein S10P---
U [auth BI]30S ribosomal protein S8P---
A [auth A7]Preprotein translocase subunit SecE