9nb6

Cryo-EM structure of the CD163/Hp(1-1)Hb complex

Method: ELECTRON MICROSCOPY Dmax: 183.8 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Scavenger receptor cysteine-rich type 1 protein M130

Homo sapiens

UniProt Q86VB7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain A; UniProt 42–1045 Chain B; UniProt 42–1045 Chain C; UniProt 42–1045 Not recorded Hemoglobin subunit alpha × 1 (P69905) Hemoglobin subunit beta × 1 (P68871) Isoform 2 of Haptoglobin × 2 (P00738) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 CA CALCIUM ION × 23 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C163A_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–1004; UniProt 42–1045 Author chain B; PDBConstruct 1–1004; UniProt 42–1045 Author chain C; PDBConstruct 1–1004; UniProt 42–1045

Hemoglobin subunit alpha

OrganismNot specified

UniProt P69905

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain D; UniProt 1–142 Not recorded Scavenger receptor cysteine-rich type 1 protein M130 × 3 (Q86VB7) Hemoglobin subunit beta × 1 (P68871) Isoform 2 of Haptoglobin × 2 (P00738) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 CA CALCIUM ION × 23 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

348 other PDB entries and 412 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HBA_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 1–142; UniProt 1–142

Hemoglobin subunit beta

OrganismNot specified

UniProt P68871

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain E; UniProt 1–147 Not recorded Scavenger receptor cysteine-rich type 1 protein M130 × 3 (Q86VB7) Hemoglobin subunit alpha × 1 (P69905) Isoform 2 of Haptoglobin × 2 (P00738) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 CA CALCIUM ION × 23 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

343 other PDB entries and 399 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HBB_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 1–147; UniProt 1–147

Isoform 2 of Haptoglobin

OrganismNot specified

UniProt P00738

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain F; UniProt 1–347 Chain G; UniProt 1–347 Not recorded Scavenger receptor cysteine-rich type 1 protein M130 × 3 (Q86VB7) Hemoglobin subunit alpha × 1 (P69905) Hemoglobin subunit beta × 1 (P68871) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 CA CALCIUM ION × 23 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

14 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HPT_HUMAN
Isoform P00738-2
PDB entities 4
Chains and sequence ranges Author chain F; PDBConstruct 1–347; UniProt 1–347 Author chain G; PDBConstruct 1–347; UniProt 1–347

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9nb6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9nb6
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id9nb6
Deposition date deposition_date2025-02-13
Structure title titleCryo-EM structure of the CD163/Hp(1-1)Hb complex
Keywords keywordsCD163, M130, Scavenger receptor, Haptoglobin, Hemoglobin, Hb, Hp, HpHb, Hp(1-1)Hb, hemolysis, ENDOCYTOSIS; ENDOCYTOSIS
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier56.97
Radius of gyration Rg (electron density) rg_electron56.48
Forward intensity I(0) i01904220000.00
Molecular weight molecular_weight343610.0 kDa
Excluded volume excluded_volume420440 ų
Envelope volume envelope_volume700830 ų
Hydration-shell volume shell_volume103910 ų
Envelope diameter envelope_diameter199.7
Shell Rg shell_rg61.78
Envelope Rg envelope_rg52.81
Shape Rg shape_rg56.46
Total Rg total_rg56.67
Total atoms total_atoms24003
Residues n_residues3122
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax183.8
Rg (real space) rg_real56.65
Rg uncertainty (real space) rg_real_error1.66
I(0) (real space) i0_real1.9040e+09
I(0) uncertainty (real space) i0_real_error3.6540e+07
Rg (reciprocal space) rg_reciprocal57.23
I(0) (reciprocal space) i0_reciprocal1906000000.0000
Solution quality estimate total_estimate0.8556
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary78.8
Skewness Skewness skewness0.048
Kurtosis Kurtosis kurtosis-0.299
Angular range angular_range— – 0.1400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha88010000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.763; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.864

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

8. Citations (1)

9. Files and Curves (10)