9FHB

Cryo-EM structure of human CD163 SRCR2-4 in complex with haptoglobin-hemoglobin

PDB DOI: https://doi.org/10.2210/pdb9FHB/pdb
EM Map EMD-50444: EMDB EMDataResource

Classification: ENDOCYTOSIS
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2024-05-27 Released: 2024-12-18
Deposition Author(s): Andersen, C.B.F., Kollman, J.M.
Funding Organization(s): Lundbeckfonden

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.87 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

The structure of human scavenger receptor CD163 in complex with haptoglobin-hemoglobin discloses the molecular mechanism for hemoglobin scavenging.

Etzerodt, E., Mikkelsen, J.H., Torvund-Jensen, M., Hennig, D., Boesen, T., Graversen, J.H., Moestrup, S.K., Kollman, J.M., Andersen, C.B.F.

To be published.

Macromolecule Content

Total Structure Weight: 204.14 kDa
Atom Count: 6,751
Modelled Residue Count: 862
Deposited Residue Count: 1,851
Unique protein chains: 4

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	A	142	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens) Explore P69905 Go to UniProtKB: P69905
PHAROS: P69905 GTEx: ENSG00000188536 ENSG00000206172
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69905
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B	147	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens) Explore P68871 Go to UniProtKB: P68871
PHAROS: P68871 GTEx: ENSG00000244734
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68871
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Haptoglobin	C	406	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P00738 (Homo sapiens) Explore P00738 Go to UniProtKB: P00738
PHAROS: P00738 GTEx: ENSG00000257017
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00738
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain C	Go to GlyGen: P00738-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Scavenger receptor cysteine-rich type 1 protein M130	D	1,156	Homo sapiens	Mutation(s): 0 Gene Names: CD163, M130
UniProt & NIH Common Fund Data Resources
Find proteins for Q86VB7 (Homo sapiens) Explore Q86VB7 Go to UniProtKB: Q86VB7
PHAROS: Q86VB7 GTEx: ENSG00000177575
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q86VB7
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain D	Go to GlyGen: Q86VB7-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain H [auth C] SDF format, chain K [auth D] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C] MOL2 format, chain K [auth D] mmCIF format, chain G [auth C] mmCIF format, chain H [auth C] mmCIF format, chain K [auth D]	G [auth C], H [auth C], K [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth C] Focus chain H [auth C] Focus chain K [auth D] Interactions & Density Focus chain G [auth C] Focus chain H [auth C] Focus chain K [auth D]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain J [auth D] MOL2 format, chain I [auth D] MOL2 format, chain J [auth D] mmCIF format, chain I [auth D] mmCIF format, chain J [auth D]	I [auth D], J [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth D] Focus chain J [auth D] Interactions & Density Focus chain I [auth D] Focus chain J [auth D]