8QI7 | pdb_00008qi7

Cryo-EM Structure of Human Serine Hydroxymethyltransferase, isoform 2 (SHMT2)

PDB DOI: https://doi.org/10.2210/pdb8QI7/pdb
EM Map EMD-18436: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2023-09-11 Released: 2023-09-20
Deposition Author(s): Rutkiewicz, M., Tran, L.H., Ruszkowski, M.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8QI7

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

Literature

New Structural Models of SHMT2

Rutkiewicz, M., Tran, L.H., Ruszkowski, M.

To be published.

Macromolecule Content

Total Structure Weight: 211.78 kDa
Atom Count: 14,609
Modeled Residue Count: 1,848
Deposited Residue Count: 1,904
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase, mitochondrial	A, B [auth D], C [auth B], D [auth C]	476	Homo sapiens	Mutation(s): 0 Gene Names: SHMT2 EC: 2.1.2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P34897 (Homo sapiens) Explore P34897 Go to UniProtKB: P34897
PHAROS: P34897 GTEx: ENSG00000182199
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P34897
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B [auth D], C [auth B], D [auth C]	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20
RECONSTRUCTION	cryoSPARC	4.0.3

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-09-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Poland	--

Revision History (Full details and data files)

Version 1.0: 2023-09-20
Type: Initial release
Version 1.1: 2023-11-15
Changes: Data collection

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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.