4RTA | pdb_00004rta

Cystal structure of the Dpy30 for MLL/SET1 COMPASS H3K4 trimethylation

PDB DOI: https://doi.org/10.2210/pdb4RTA/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-11-14 Released: 2015-10-07
Deposition Author(s): Zhang, H.M., Li, M., Chang, W.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.235 (Depositor), 0.238 (DCC)
R-Value Work:
0.207 (Depositor), 0.216 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4RTA

This is version 1.1 of the entry. See complete history.

Literature

Structural implications of Dpy30 oligomerization for MLL/SET1 COMPASS H3K4 trimethylation.

Zhang, H., Li, M., Gao, Y., Jia, C., Pan, X., Cao, P., Zhao, X., Zhang, J., Chang, W.

(2015) Protein Cell 6: 147-151

PubMed: 25542209 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1007/s13238-014-0127-z
Primary Citation Related Structures:
4RT4, 4RTA

Organizational Affiliation

Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

Macromolecule Content

Total Structure Weight: 24.48 kDa
Atom Count: 1,162
Modeled Residue Count: 129
Deposited Residue Count: 212
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein dpy-30 homolog	A, B	106	Homo sapiens	Mutation(s): 0 Gene Names: DPY30
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C005 (Homo sapiens) Explore Q9C005 Go to UniProtKB: Q9C005
PHAROS: Q9C005 GTEx: ENSG00000162961
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9C005
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.235 (Depositor), 0.238 (DCC)
R-Value Work: 0.207 (Depositor), 0.216 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.579	α = 90
b = 89.579	β = 90
c = 53.202	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-10-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-10-07
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.