8QPQ | pdb_00008qpq

C1 turret to capsid interface of full Haloferax tailed virus 1 adjacent to the portal-capsid interface.

PDB DOI: https://doi.org/10.2210/pdb8QPQ/pdb
EM Map EMD-18559: EMDB EMDataResource

Classification: VIRUS
Organism(s): Haloferax tailed virus 1
Mutation(s): No

Deposited: 2023-10-02 Released: 2024-10-09
Deposition Author(s): Zhang, D., Daum, B., Isupov, M.N., McLaren, M.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

CryoEM structure of Haloferax tailed virus 1

Zhang, D., Daum, B., Isupov, M.N., McLaren, M., Oksanen, H., Quax, T.E.F., Schwarzer, S., Gold, V.A.M., Antson, A.

To be published.

Macromolecule Content

Total Structure Weight: 470.44 kDa
Atom Count: 28,263
Modelled Residue Count: 3,683
Deposited Residue Count: 4,305
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prokaryotic polysaccharide deacetylase	A [auth TC], H [auth TA], I [auth TB]	413	Haloferax tailed virus 1	Mutation(s): 0
UniProt
Find proteins for A0A410N6W3 (Haloferax tailed virus 1) Explore A0A410N6W3 Go to UniProtKB: A0A410N6W3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A410N6W3
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
gp30	B [auth TD] C [auth TE] D [auth TF] E [auth TG] F [auth TH] B [auth TD], C [auth TE], D [auth TF], E [auth TG], F [auth TH], G [auth TI]	115	Haloferax tailed virus 1	Mutation(s): 0
UniProt
Find proteins for A0A410N6V5 (Haloferax tailed virus 1) Explore A0A410N6V5 Go to UniProtKB: A0A410N6V5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A410N6V5
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HK97 gp5-like major capsid protein	J [auth LA] K [auth LB] L [auth LF] M [auth LE] N [auth LD] J [auth LA], K [auth LB], L [auth LF], M [auth LE], N [auth LD], O [auth LC]	396	Haloferax tailed virus 1	Mutation(s): 0
UniProt
Find proteins for A0A410N6T9 (Haloferax tailed virus 1) Explore A0A410N6T9 Go to UniProtKB: A0A410N6T9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A410N6T9
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain DA [auth TA] SDF format, chain FA [auth TB] SDF format, chain P [auth TC] MOL2 format, chain DA [auth TA] MOL2 format, chain FA [auth TB] MOL2 format, chain P [auth TC] mmCIF format, chain DA [auth TA] mmCIF format, chain FA [auth TB] mmCIF format, chain P [auth TC]	DA [auth TA], FA [auth TB], P [auth TC]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth TA] Focus chain FA [auth TB] Focus chain P [auth TC] Interactions & Density Focus chain DA [auth TA] Focus chain FA [auth TB] Focus chain P [auth TC]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth TH] SDF format, chain AB [auth LE] SDF format, chain BA [auth TI] SDF format, chain BB [auth LE] SDF format, chain CA [auth TI] SDF format, chain CB [auth LE] SDF format, chain DB [auth LE] SDF format, chain EA [auth TA] SDF format, chain EB [auth LD] SDF format, chain FB [auth LD] SDF format, chain GA [auth TB] SDF format, chain GB [auth LD] SDF format, chain HA [auth LA] SDF format, chain HB [auth LD] SDF format, chain IA [auth LA] SDF format, chain IB [auth LD] SDF format, chain JA [auth LA] SDF format, chain JB [auth LD] SDF format, chain KA [auth LA] SDF format, chain KB [auth LC] SDF format, chain LA SDF format, chain LB [auth LC] SDF format, chain MA [auth LA] SDF format, chain MB [auth LC] SDF format, chain NA [auth LA] SDF format, chain NB [auth LC] SDF format, chain OA [auth LB] SDF format, chain OB [auth LC] SDF format, chain PA [auth LB] SDF format, chain PB [auth LC] SDF format, chain Q [auth TC] SDF format, chain QA [auth LB] SDF format, chain R [auth TD] SDF format, chain RA [auth LB] SDF format, chain S [auth TD] SDF format, chain SA [auth LB] SDF format, chain T [auth TE] SDF format, chain TA [auth LB] SDF format, chain U [auth TE] SDF format, chain UA [auth LF] SDF format, chain V [auth TF] SDF format, chain VA [auth LF] SDF format, chain W [auth TF] SDF format, chain WA [auth LF] SDF format, chain X [auth TG] SDF format, chain XA [auth LF] SDF format, chain Y [auth TG] SDF format, chain YA [auth LF] SDF format, chain Z [auth TH] SDF format, chain ZA [auth LE] MOL2 format, chain AA [auth TH] MOL2 format, chain AB [auth LE] MOL2 format, chain BA [auth TI] MOL2 format, chain BB [auth LE] MOL2 format, chain CA [auth TI] MOL2 format, chain CB [auth LE] MOL2 format, chain DB [auth LE] MOL2 format, chain EA [auth TA] MOL2 format, chain EB [auth LD] MOL2 format, chain FB [auth LD] MOL2 format, chain GA [auth TB] MOL2 format, chain GB [auth LD] MOL2 format, chain HA [auth LA] MOL2 format, chain HB [auth LD] MOL2 format, chain IA [auth LA] MOL2 format, chain IB [auth LD] MOL2 format, chain JA [auth LA] MOL2 format, chain JB [auth LD] MOL2 format, chain KA [auth LA] MOL2 format, chain KB [auth LC] MOL2 format, chain LA MOL2 format, chain LB [auth LC] MOL2 format, chain MA [auth LA] MOL2 format, chain MB [auth LC] MOL2 format, chain NA [auth LA] MOL2 format, chain NB [auth LC] MOL2 format, chain OA [auth LB] MOL2 format, chain OB [auth LC] MOL2 format, chain PA [auth LB] MOL2 format, chain PB [auth LC] MOL2 format, chain Q [auth TC] MOL2 format, chain QA [auth LB] MOL2 format, chain R [auth TD] MOL2 format, chain RA [auth LB] MOL2 format, chain S [auth TD] MOL2 format, chain SA [auth LB] MOL2 format, chain T [auth TE] MOL2 format, chain TA [auth LB] MOL2 format, chain U [auth TE] MOL2 format, chain UA [auth LF] MOL2 format, chain V [auth TF] MOL2 format, chain VA [auth LF] MOL2 format, chain W [auth TF] MOL2 format, chain WA [auth LF] MOL2 format, chain X [auth TG] MOL2 format, chain XA [auth LF] MOL2 format, chain Y [auth TG] MOL2 format, chain YA [auth LF] MOL2 format, chain Z [auth TH] MOL2 format, chain ZA [auth LE] mmCIF format, chain AA [auth TH] mmCIF format, chain AB [auth LE] mmCIF format, chain BA [auth TI] mmCIF format, chain BB [auth LE] mmCIF format, chain CA [auth TI] mmCIF format, chain CB [auth LE] mmCIF format, chain DB [auth LE] mmCIF format, chain EA [auth TA] mmCIF format, chain EB [auth LD] mmCIF format, chain FB [auth LD] mmCIF format, chain GA [auth TB] mmCIF format, chain GB [auth LD] mmCIF format, chain HA [auth LA] mmCIF format, chain HB [auth LD] mmCIF format, chain IA [auth LA] mmCIF format, chain IB [auth LD] mmCIF format, chain JA [auth LA] mmCIF format, chain JB [auth LD] mmCIF format, chain KA [auth LA] mmCIF format, chain KB [auth LC] mmCIF format, chain LA mmCIF format, chain LB [auth LC] mmCIF format, chain MA [auth LA] mmCIF format, chain MB [auth LC] mmCIF format, chain NA [auth LA] mmCIF format, chain NB [auth LC] mmCIF format, chain OA [auth LB] mmCIF format, chain OB [auth LC] mmCIF format, chain PA [auth LB] mmCIF format, chain PB [auth LC] mmCIF format, chain Q [auth TC] mmCIF format, chain QA [auth LB] mmCIF format, chain R [auth TD] mmCIF format, chain RA [auth LB] mmCIF format, chain S [auth TD] mmCIF format, chain SA [auth LB] mmCIF format, chain T [auth TE] mmCIF format, chain TA [auth LB] mmCIF format, chain U [auth TE] mmCIF format, chain UA [auth LF] mmCIF format, chain V [auth TF] mmCIF format, chain VA [auth LF] mmCIF format, chain W [auth TF] mmCIF format, chain WA [auth LF] mmCIF format, chain X [auth TG] mmCIF format, chain XA [auth LF] mmCIF format, chain Y [auth TG] mmCIF format, chain YA [auth LF] mmCIF format, chain Z [auth TH] mmCIF format, chain ZA [auth LE]	AA [auth TH] AB [auth LE] BA [auth TI] BB [auth LE] CA [auth TI] AA [auth TH], AB [auth LE], BA [auth TI], BB [auth LE], CA [auth TI], CB [auth LE], DB [auth LE], EA [auth TA], EB [auth LD], FB [auth LD], GA [auth TB], GB [auth LD], HA [auth LA], HB [auth LD], IA [auth LA], IB [auth LD], JA [auth LA], JB [auth LD], KA [auth LA], KB [auth LC], LA, LB [auth LC], MA [auth LA], MB [auth LC], NA [auth LA], NB [auth LC], OA [auth LB], OB [auth LC], PA [auth LB], PB [auth LC], Q [auth TC], QA [auth LB], R [auth TD], RA [auth LB], S [auth TD], SA [auth LB], T [auth TE], TA [auth LB], U [auth TE], UA [auth LF], V [auth TF], VA [auth LF], W [auth TF], WA [auth LF], X [auth TG], XA [auth LF], Y [auth TG], YA [auth LF], Z [auth TH], ZA [auth LE]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth TH] Focus chain AB [auth LE] Focus chain BA [auth TI] Focus chain BB [auth LE] Focus chain CA [auth TI] Focus chain CB [auth LE] Focus chain DB [auth LE] Focus chain EA [auth TA] Focus chain EB [auth LD] Focus chain FB [auth LD] Focus chain GA [auth TB] Focus chain GB [auth LD] Focus chain HA [auth LA] Focus chain HB [auth LD] Focus chain IA [auth LA] Focus chain IB [auth LD] Focus chain JA [auth LA] Focus chain JB [auth LD] Focus chain KA [auth LA] Focus chain KB [auth LC] Focus chain LA Focus chain LB [auth LC] Focus chain MA [auth LA] Focus chain MB [auth LC] Focus chain NA [auth LA] Focus chain NB [auth LC] Focus chain OA [auth LB] Focus chain OB [auth LC] Focus chain PA [auth LB] Focus chain PB [auth LC] Focus chain Q [auth TC] Focus chain QA [auth LB] Focus chain R [auth TD] Focus chain RA [auth LB] Focus chain S [auth TD] Focus chain SA [auth LB] Focus chain T [auth TE] Focus chain TA [auth LB] Focus chain U [auth TE] Focus chain UA [auth LF] Focus chain V [auth TF] Focus chain VA [auth LF] Focus chain W [auth TF] Focus chain WA [auth LF] Focus chain X [auth TG] Focus chain XA [auth LF] Focus chain Y [auth TG] Focus chain YA [auth LF] Focus chain Z [auth TH] Focus chain ZA [auth LE] Interactions & Density Focus chain AA [auth TH] Focus chain AB [auth LE] Focus chain BA [auth TI] Focus chain BB [auth LE] Focus chain CA [auth TI] Focus chain CB [auth LE] Focus chain DB [auth LE] Focus chain EA [auth TA] Focus chain EB [auth LD] Focus chain FB [auth LD] Focus chain GA [auth TB] Focus chain GB [auth LD] Focus chain HA [auth LA] Focus chain HB [auth LD] Focus chain IA [auth LA] Focus chain IB [auth LD] Focus chain JA [auth LA] Focus chain JB [auth LD] Focus chain KA [auth LA] Focus chain KB [auth LC] Focus chain LA Focus chain LB [auth LC] Focus chain MA [auth LA] Focus chain MB [auth LC] Focus chain NA [auth LA] Focus chain NB [auth LC] Focus chain OA [auth LB] Focus chain OB [auth LC] Focus chain PA [auth LB] Focus chain PB [auth LC] Focus chain Q [auth TC] Focus chain QA [auth LB] Focus chain R [auth TD] Focus chain RA [auth LB] Focus chain S [auth TD] Focus chain SA [auth LB] Focus chain T [auth TE] Focus chain TA [auth LB] Focus chain U [auth TE] Focus chain UA [auth LF] Focus chain V [auth TF] Focus chain VA [auth LF] Focus chain W [auth TF] Focus chain WA [auth LF] Focus chain X [auth TG] Focus chain XA [auth LF] Focus chain Y [auth TG] Focus chain YA [auth LF] Focus chain Z [auth TH] Focus chain ZA [auth LE]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NEP Query on NEP	B [auth TD] C [auth TE] D [auth TF] E [auth TG] F [auth TH] B [auth TD], C [auth TE], D [auth TF], E [auth TG], F [auth TH], G [auth TI]	L-PEPTIDE LINKING	C₆ H₁₀ N₃ O₅ P		HIS