9HT6 | pdb_00009ht6

Crystal structure of Tetraspanin CD82 Large Extracellular Loop (LEL)

PDB DOI: https://doi.org/10.2210/pdb9HT6/pdb

Classification: ENDOCYTOSIS
Organism(s): Homo sapiens
Expression System: Drosophila melanogaster
Mutation(s): Yes

Deposited: 2024-12-19 Released: 2025-11-19
Deposition Author(s): Nagarathinam, K., Krey, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.276 (Depositor), 0.276 (DCC)
R-Value Work:
0.226 (Depositor), 0.227 (DCC)
R-Value Observed:
0.229 (Depositor)

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

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

Literature

Crystal structure of Tetraspanin CD82 Large Extracellular Loop (LEL)

Nagarathinam, K., Krey, T.

To be published.

Macromolecule Content

Total Structure Weight: 28.93 kDa
Atom Count: 1,906
Modeled Residue Count: 239
Deposited Residue Count: 246
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CD82 antigen	A, B	123	Homo sapiens	Mutation(s): 3 Gene Names: CD82, KAI1, SAR2, ST6, TSPAN27
UniProt & NIH Common Fund Data Resources
Find proteins for P27701 (Homo sapiens) Explore P27701 Go to UniProtKB: P27701
PHAROS: P27701 GTEx: ENSG00000085117
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27701
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] 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] F [auth B] G [auth B] C [auth A], D [auth A], E [auth B], F [auth B], G [auth B], H [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.276 (Depositor), 0.276 (DCC)
R-Value Work: 0.226 (Depositor), 0.227 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.42	α = 90
b = 62.67	β = 90
c = 97.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
SHELXDE	phasing
Coot	model building
BUCCANEER	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-19

Deposition Author(s):

Nagarathinam, K.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-11-19
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.