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)

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Experimental Data Snapshot

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

Literature

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

Shu, Z.M., Duan, J.S., Zhou, A.W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A4B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A6B1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

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

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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P13224-1

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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P14770-1

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

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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
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

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-25 
Deposition Author(s): Shu, Z.M., Duan, J.S., Zhou, A.W.

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

Revision History  

• Version 1.0: 2024-12-25
  Type: Initial release
  
• Version 1.1: 2025-07-02
  Changes: Data collection