6P7J | pdb_00006p7j

Crystal structure of Latency Associated Peptide unbound to TGF-beta1

PDB DOI: https://doi.org/10.2210/pdb6P7J/pdb

Classification: CYTOKINE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2019-06-05 Released: 2020-03-11
Deposition Author(s): Stachowski, T.R., Snell, M.E., Snell, E.H.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.322 (Depositor), 0.323 (DCC)
R-Value Work:
0.288 (Depositor), 0.288 (DCC)
R-Value Observed:
0.290 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural insights into conformational switching in latency-associated peptide between transforming growth factor beta-1 bound and unbound states

Stachowski, T.R., Snell, M.E., Snell, E.H.

(2020) IUCrJ 7: 238-252

DOI: https://doi.org/10.1107/S205225251901707X

Macromolecule Content

Total Structure Weight: 29.27 kDa
Atom Count: 1,298
Modeled Residue Count: 159
Deposited Residue Count: 255
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transforming growth factor beta-1 proprotein	A	255	Homo sapiens	Mutation(s): 1 Gene Names: TGFB1, TGFB
UniProt & NIH Common Fund Data Resources
Find proteins for P01137 (Homo sapiens) Explore P01137 Go to UniProtKB: P01137
PHAROS: P01137 GTEx: ENSG00000105329
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01137
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.322 (Depositor), 0.323 (DCC)
R-Value Work: 0.288 (Depositor), 0.288 (DCC)
R-Value Observed: 0.290 (Depositor)

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.06	α = 90
b = 154.9	β = 90
c = 62.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MR-Rosetta	phasing
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-03-11

Deposition Author(s):

Stachowski, T.R.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1231306

Revision History (Full details and data files)

Version 1.0: 2020-03-11
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

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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.