6VCS | pdb_00006vcs

SRA domain of UHRF1 in complex with DNA

• PDB DOI: https://doi.org/10.2210/pdb6VCS/pdb
• NAKB: 6VCS

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-22 Released: 2020-03-04 
• Deposition Author(s): Dong, C., Tempel, W., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Min, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: experimental

Literature

SRA domain of UHRF1 in complex with DNA

Dong, C., Tempel, W., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Min, J., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 78.95 kDa 
• Atom Count: 5,084 
• Modeled Residue Count: 595 
• Deposited Residue Count: 663 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase UHRF1	A, B, E	211	Homo sapiens	Mutation(s): 0  Gene Names: UHRF1, ICBP90, NP95, RNF106 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q96T88 (Homo sapiens) Explore Q96T88  Go to UniProtKB:  Q96T88
PHAROS:  Q96T88 GTEx:  ENSG00000276043

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
UNK-UNK-UNK-UNK	F [auth G]	6	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*CP*TP*GP*TP*AP*CP*AP*GP*GP*C)-3')	C, D	12	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	AA [auth A], AB [auth B], BA [auth A], BB [auth B], CA [auth A], CB [auth B], DA [auth A], DB [auth B], EA [auth A], EB [auth B], FA [auth A], FB [auth B], G [auth A], GA [auth A], GB [auth B], H [auth A], HA [auth A], HB [auth B], I [auth A], IA [auth A], IB [auth E], J [auth A], JA [auth B], JB [auth E], K [auth A], KA [auth B], KB [auth E], L [auth A], LA [auth B], LB [auth E], M [auth A], MA [auth B], MB [auth E], N [auth A], NA [auth B], NB [auth E], O [auth A], OA [auth B], OB [auth E], P [auth A], PA [auth B], PB [auth E], Q [auth A], QA [auth B], QB [auth E], R [auth A], RA [auth B], RB [auth E], S [auth A], SA [auth B], SB [auth E], T [auth A], TA [auth B], TB [auth E], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A], ZA [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36vcs

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.995	α = 90
b = 113.809	β = 90
c = 133.946	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-04 
Deposition Author(s): Dong, C., Tempel, W., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2020-03-04
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary