8WFS | pdb_00008wfs

Cryo-EM structure of GPIb-IX Complex

PDB DOI: https://doi.org/10.2210/pdb8WFS/pdb
EM Map EMD-37498: EMDB EMDataResource

Classification: BLOOD CLOTTING
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes
Membrane Protein: Yes PDBTM

Deposited: 2023-09-20 Released: 2024-12-25
Deposition Author(s): Shu, Z.M., Duan, J.S., Zhou, A.W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.36 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8WFS

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

Literature

Cryo-Structure of GPIb-IX complex at 3.36 Angstroms resolution

Shu, Z.M., Duan, J.S., Zhou, A.W.

To be published.

Macromolecule Content

Total Structure Weight: 141.25 kDa
Atom Count: 6,274
Modeled Residue Count: 808
Deposited Residue Count: 1,290
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet glycoprotein Ib beta chain	A [auth c], B [auth C], D [auth B], E [auth b]	192	Homo sapiens	Mutation(s): 1 Gene Names: GP1BB Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P13224 (Homo sapiens) Explore P13224 Go to UniProtKB: P13224
PHAROS: P13224
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13224
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth c] Focus chain B [auth C] Focus chain D [auth B] Focus chain E [auth b]	Go to GlyGen: P13224-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet glycoprotein IX	C [auth E], F [auth X]	191	Homo sapiens	Mutation(s): 1 Gene Names: GP9 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P14770 (Homo sapiens) Explore P14770 Go to UniProtKB: P14770
PHAROS: P14770 GTEx: ENSG00000169704
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14770
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C [auth E] Focus chain F [auth X]	Go to GlyGen: P14770-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet glycoprotein Ib alpha chain	G [auth a]	140	Homo sapiens	Mutation(s): 2 Gene Names: GP1BA Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P07359 (Homo sapiens) Explore P07359 Go to UniProtKB: P07359
PHAROS: P07359 GTEx: ENSG00000185245
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07359
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth A], I [auth D], L [auth H], M [auth I]	2		N-Glycosylation	Interactions Focus chain H [auth A] Focus chain I [auth D] Focus chain L [auth H] Focus chain M [auth I] Interactions & Density Focus chain H [auth A] Focus chain I [auth D] Focus chain L [auth H] Focus chain M [auth I]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth F], K [auth G]	3		N-Glycosylation	Interactions Focus chain J [auth F] Focus chain K [auth G] Interactions & Density Focus chain J [auth F] Focus chain K [auth G]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.36 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-25

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2024-12-25
Type: Initial release
Version 1.1: 2025-07-02
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.