9CWM | pdb_00009cwm

Cryo-EM structure of human Low-density lipoprotein receptor-related protein 2

PDB DOI: https://doi.org/10.2210/pdb9CWM/pdb
EM Map EMD-45967: EMDB EMDataResource

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

Deposited: 2024-07-29 Released: 2025-08-06
Deposition Author(s): Zhang, Z., Lyu, M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 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 human Low-density lipoprotein receptor-related protein 2

Zhang, Z., Lyu, M.

To be published.

Macromolecule Content

Total Structure Weight: 1,056.64 kDa
Atom Count: 58,072
Modeled Residue Count: 7,387
Deposited Residue Count: 9,310
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low-density lipoprotein receptor-related protein 2	A, B	4,655	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P98164 (Homo sapiens) Explore P98164 Go to UniProtKB: P98164
PHAROS: P98164 GTEx: ENSG00000081479
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P98164
Glycosylation
Glycosylation Sites: 17	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P98164-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
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	C, D, E, F, I C, D, E, F, I, J, K, L, N	3		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Focus chain F Focus chain I Focus chain J Focus chain K Focus chain L Focus chain N Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F Focus chain I Focus chain J Focus chain K Focus chain L Focus chain N
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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	G, H, M	2		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain M Interactions & Density Focus chain G Focus chain H Focus chain M
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain T [auth A] SDF format, chain V [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain W [auth A] SDF format, chain U [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain KA [auth B] SDF format, chain JA [auth B] SDF format, chain IA [auth B] SDF format, chain HA [auth B] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain T [auth A] MOL2 format, chain V [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain W [auth A] MOL2 format, chain U [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain T [auth A] mmCIF format, chain V [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain W [auth A] mmCIF format, chain U [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth B], KA [auth B], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]