9L21 | pdb_00009l21

cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with factor IX

PDB DOI: https://doi.org/10.2210/pdb9L21/pdb
EM Map EMD-62765: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-12-16 Released: 2025-10-22
Deposition Author(s): Yao, D., Wu, K., Lan, P.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.62 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with factor IX

Yao, D., Wu, K., Lan, P.

To be published.

Macromolecule Content

Total Structure Weight: 89.48 kDa
Atom Count: 6,162
Modeled Residue Count: 702
Deposited Residue Count: 726
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin K-dependent gamma-carboxylase	A	698	Homo sapiens	Mutation(s): 0 Gene Names: GGCX, GC EC: 4.1.1.90
UniProt & NIH Common Fund Data Resources
Find proteins for P38435 (Homo sapiens) Explore P38435 Go to UniProtKB: P38435
PHAROS: P38435 GTEx: ENSG00000115486
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38435
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A	Go to GlyGen: P38435-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor IX	B	28	Homo sapiens	Mutation(s): 0 Gene Names: F9 EC: 3.4.21.22
UniProt & NIH Common Fund Data Resources
Find proteins for P00740 (Homo sapiens) Explore P00740 Go to UniProtKB: P00740
PHAROS: P00740 GTEx: ENSG00000101981
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00740
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEE Query on PEE Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A], M [auth A]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A]
Y01 Query on Y01 Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
A1AVC (Subject of Investigation/LOI) Query on A1AVC Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	vitamin K1 hydroquinone C₃₁ H₄₈ O₂ BUFJIHPUGZHTHL-NKFFZRIASA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
BCT Query on BCT Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CO2 Query on CO2 Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	CARBON DIOXIDE C O₂ CURLTUGMZLYLDI-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]