6U90 | pdb_00006u90

Crystal structure of DNMT3B(N779A)-DNMT3L in complex with CpGpT DNA

  • Classification: Transferase/DNA
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2019-09-06 Released: 2020-06-10 
  • Deposition Author(s): Gao, L., Song, J.
  • Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.259 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms

Gao, L.

To be published.

Macromolecule Content 

  • Total Structure Weight: 130.97 kDa 
  • Atom Count: 8,631 
  • Modeled Residue Count: 1,018 
  • Deposited Residue Count: 1,050 
  • Unique protein chains: 2
  • Unique nucleic acid chains: 1

Macromolecules


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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 3B
A, D
291Homo sapiensMutation(s): 1 
Gene Names: DNMT3B
EC: 2.1.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBC3 (Homo sapiens)
Explore Q9UBC3 
Go to UniProtKB:  Q9UBC3
PHAROS:  Q9UBC3
GTEx:  ENSG00000088305 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBC3
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 3-like
B, C
209Homo sapiensMutation(s): 0 
Gene Names: DNMT3L
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJW3 (Homo sapiens)
Explore Q9UJW3 
Go to UniProtKB:  Q9UJW3
PHAROS:  Q9UJW3
GTEx:  ENSG00000142182 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UJW3
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
CpGpT DNA (25-MER)
E, F
25Homo sapiens
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.259 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 191.506α = 90
b = 191.506β = 90
c = 49.597γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States1R35GM119721

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-12-25
    Changes: Advisory, Data collection, Derived calculations, Structure summary