4HFX | pdb_00004hfx

Crystal structure of a transcription elongation factor B polypeptide 3 from Homo sapiens, Northeast Structural Genomics consortium target id HR4748B.

PDB DOI: https://doi.org/10.2210/pdb4HFX/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2012-10-05 Released: 2012-12-12
Deposition Author(s): Seetharaman, J., Su, M., Ciccosanti, C., Sahdev, S., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free:
0.263 (Depositor), 0.268 (DCC)
R-Value Work:
0.235 (Depositor), 0.232 (DCC)
R-Value Observed:
0.236 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4HFX

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

Literature

Crystal structure of a transcription elongation factor B polypeptide 3 from Homo sapiens, Northeast Structural Genomics consortium target id HR4748B. (CASP Target)

Seetharaman, J., Su, M., Ciccosanti, C., Sahdev, S., Acton, T.B., Xiao, R., K Everett, J., T Montelione, G., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 48.87 kDa
Atom Count: 1,872
Modeled Residue Count: 223
Deposited Residue Count: 388
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor B polypeptide 3	A, B, C, D	97	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q14241 (Homo sapiens) Explore Q14241 Go to UniProtKB: Q14241
PHAROS: Q14241 GTEx: ENSG00000011007
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14241
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain F [auth C] SDF format, chain E [auth B] MOL2 format, chain G [auth D] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] mmCIF format, chain G [auth D] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B]	E [auth B], F [auth C], G [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth B] Focus chain F [auth C] Focus chain G [auth D] Interactions & Density Focus chain E [auth B] Focus chain F [auth C] Focus chain G [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free: 0.263 (Depositor), 0.268 (DCC)
R-Value Work: 0.235 (Depositor), 0.232 (DCC)
R-Value Observed: 0.236 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.643	α = 90
b = 80.643	β = 90
c = 63.222	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-12-12

Deposition Author(s):

Seetharaman, J.

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2012-12-12
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references, Structure summary
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.