8XMQ

Structure of dimeric CD163 in complex with Hb-Hp

PDB DOI: https://doi.org/10.2210/pdb8XMQ/pdb
EM Map EMD-38486: EMDB EMDataResource

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

Deposited: 2023-12-27 Released: 2025-01-01
Deposition Author(s): Xu, H., Su, X.D.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.21 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

Structure of dimeric CD163 in complex with Hb-Hp

Xu, H., Su, X.D.

To be published.

Macromolecule Content

Total Structure Weight: 292.26 kDa
Atom Count: 12,950
Modelled Residue Count: 1,657
Deposited Residue Count: 2,654
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Haptoglobin	A [auth 2]	347	Homo sapiens	Mutation(s): 0 Gene Names: HP
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: 3	Glycosylation Focus chain A [auth 2]	Go to GlyGen: P00738-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Scavenger receptor cysteine-rich type 1 protein M130	B [auth F], C [auth D]	1,009	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: 3	Glycosylation Focus chain B [auth F] Focus chain C [auth D]	Go to GlyGen: Q86VB7-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	D [auth C]	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

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	E [auth G]	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

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth Y], G [auth A]	2		N-Glycosylation	Interactions Focus chain F [auth Y] Focus chain G [auth A] Interactions & Density Focus chain F [auth Y] Focus chain G [auth A]

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth G] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth G] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth G]	AA [auth C], BA [auth G]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AA [auth C] Focus chain BA [auth G] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth G]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain H [auth 2] SDF format, chain I [auth 2] SDF format, chain P [auth F] SDF format, chain Q [auth F] SDF format, chain R [auth F] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain H [auth 2] MOL2 format, chain I [auth 2] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth F] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] mmCIF format, chain H [auth 2] mmCIF format, chain I [auth 2] mmCIF format, chain P [auth F] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth F] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D]	H [auth 2] I [auth 2] P [auth F] Q [auth F] R [auth F] H [auth 2], I [auth 2], P [auth F], Q [auth F], R [auth F], S [auth D], T [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth 2] Focus chain I [auth 2] Focus chain P [auth F] Focus chain Q [auth F] Focus chain R [auth F] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain H [auth 2] Focus chain I [auth 2] Focus chain P [auth F] Focus chain Q [auth F] Focus chain R [auth F] Focus chain S [auth D] Focus chain T [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain J [auth F] SDF format, chain K [auth F] SDF format, chain L [auth F] SDF format, chain M [auth F] SDF format, chain N [auth F] SDF format, chain O [auth F] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain J [auth F] MOL2 format, chain K [auth F] MOL2 format, chain L [auth F] MOL2 format, chain M [auth F] MOL2 format, chain N [auth F] MOL2 format, chain O [auth F] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain J [auth F] mmCIF format, chain K [auth F] mmCIF format, chain L [auth F] mmCIF format, chain M [auth F] mmCIF format, chain N [auth F] mmCIF format, chain O [auth F] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	J [auth F] K [auth F] L [auth F] M [auth F] N [auth F] J [auth F], K [auth F], L [auth F], M [auth F], N [auth F], O [auth F], U [auth D], V [auth D], W [auth D], X [auth D], Y [auth D], Z [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth F] Focus chain K [auth F] Focus chain L [auth F] Focus chain M [auth F] Focus chain N [auth F] Focus chain O [auth F] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain J [auth F] Focus chain K [auth F] Focus chain L [auth F] Focus chain M [auth F] Focus chain N [auth F] Focus chain O [auth F] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]