12NP | pdb_000012np

Crystal structure of the CD7 ectodomain bound to K12

PDB DOI: https://doi.org/10.2210/pdb12NP/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-04-13 Released: 2026-05-06
Deposition Author(s): Mcshan, A.C., Miles, U.Z.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.278 (Depositor), 0.278 (DCC)
R-Value Work:
0.241 (Depositor), 0.241 (DCC)
R-Value Observed:
0.243 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 12NP

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the CD7 ectodomain bound to K12

Mcshan, A.C., Miles, U.Z.

To be published.

Macromolecule Content

Total Structure Weight: 100.56 kDa
Atom Count: 7,077
Modeled Residue Count: 889
Deposited Residue Count: 916
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Secreted and transmembrane protein 1	A [auth B], B [auth A], E [auth F], G [auth H]	109	Homo sapiens	Mutation(s): 0 Gene Names: SECTM1, K12
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WVN6 (Homo sapiens) Explore Q8WVN6 Go to UniProtKB: Q8WVN6
PHAROS: Q8WVN6 GTEx: ENSG00000141574
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WVN6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell antigen CD7	C, D, F [auth G], H [auth E]	120	Homo sapiens	Mutation(s): 0 Gene Names: CD7
UniProt & NIH Common Fund Data Resources
Find proteins for P09564 (Homo sapiens) Explore P09564 Go to UniProtKB: P09564
PHAROS: P09564 GTEx: ENSG00000173762
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09564
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.278 (Depositor), 0.278 (DCC)
R-Value Work: 0.241 (Depositor), 0.241 (DCC)
R-Value Observed: 0.243 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.681	α = 90
b = 121.95	β = 102.99
c = 88.871	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	United States	GR00027161

Revision History (Full details and data files)

Version 1.0: 2026-05-06
Type: Initial release

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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.