9GMR

SIRT7-H3K36MTUnucleosome complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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

Structural basis of SIRT7 nucleosome engagement and substrate specificity

Carlos, M.Y.Babatunde, E.Polina, F.Esther, S.Dongchun, N.Henning, S.Beat, F.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2
A, E
136Homo sapiensMutation(s): 0 
Gene Names: H3C15HIST2H3AH3C14H3F2H3FMHIST2H3CH3C13HIST2H3D
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Find proteins for Q71DI3 (Homo sapiens)
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PHAROS:  Q71DI3
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UniProt GroupQ71DI3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
103Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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PHAROS:  P62805
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UniProt GroupP62805
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 2-A
C, G
129Homo sapiensMutation(s): 0 
Gene Names: HIST2H2AA3H2AFOHIST2H2AAHIST2H2AA4
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Find proteins for Q6FI13 (Homo sapiens)
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PHAROS:  Q6FI13
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UniProt GroupQ6FI13
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-J
D, H
126Homo sapiensMutation(s): 0 
Gene Names: H2BC11H2BFRHIST1H2BJ
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Find proteins for P06899 (Homo sapiens)
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PHAROS:  P06899
GTEx:  ENSG00000124635 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-7401Homo sapiensMutation(s): 0 
Gene Names: SIRT7SIR2L7
EC: 2.3.1.286 (PDB Primary Data), 2.3.1 (PDB Primary Data)
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Find proteins for Q9NRC8 (Homo sapiens)
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PHAROS:  Q9NRC8
GTEx:  ENSG00000187531 
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (149-MER)149Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (149-MER)149Homo sapiens
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IY0 (Subject of Investigation/LOI)
Query on A1IY0

Download Ideal Coordinates CCD File 
L [auth A][[(2~{R},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-2-(methylamino)-6-oxidanyl-2-(propylamino)-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
C20 H33 N7 O13 P2 S
RTLOVKKJOOOFSD-SUAKPWHCSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
M [auth K]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland#TMPFP2_217187
Independent Research Fund Denmark - Medical SciencesDenmark#2028.00011B
Swiss National Science FoundationSwitzerlandIZLCZO_206089
La Caixa FoundationSpain100010434

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release