9fmu

Cryo-EM structure of human CD163 SRCR1-9 in complex with haptoglobin-hemoglobin

Method: ELECTRON MICROSCOPY Dmax: 157.1 Å Quality: REASONABLE

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

Hemopressin

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–142 Not recorded Spinorphin × 1 (P68871) Isoform 2 of Haptoglobin × 1 (P00738) Scavenger receptor cysteine-rich type 1 protein M130 × 2 (Q86VB7) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CA CALCIUM ION × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.46 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 1
Chains and sequence ranges Author chain A; PDBConstruct 1–142; UniProt 1–142

Spinorphin

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 1–147 Not recorded Hemopressin × 1 (P69905) Isoform 2 of Haptoglobin × 1 (P00738) Scavenger receptor cysteine-rich type 1 protein M130 × 2 (Q86VB7) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CA CALCIUM ION × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.46 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 2
Chains and sequence ranges Author chain B; 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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 1–347 Not recorded Hemopressin × 1 (P69905) Spinorphin × 1 (P68871) Scavenger receptor cysteine-rich type 1 protein M130 × 2 (Q86VB7) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CA CALCIUM ION × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.46 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 3
Chains and sequence ranges Author chain C; PDBConstruct 1–347; UniProt 1–347

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 1–1036 Chain E; UniProt 1–1036 Not recorded Hemopressin × 1 (P69905) Spinorphin × 1 (P68871) Isoform 2 of Haptoglobin × 1 (P00738) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CA CALCIUM ION × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.46 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 4
Chains and sequence ranges Author chain D; PDBConstruct 1–1036; UniProt 1–1036 Author chain E; PDBConstruct 1–1036; UniProt 1–1036

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 9fmu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9fmu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9fmu
Deposition date deposition_date2024-06-07
Structure title titleCryo-EM structure of human CD163 SRCR1-9 in complex with haptoglobin-hemoglobin
Keywords keywordsScavenging receptor, oxygen transport, complex, hemolysis, inflammation, ENDOCYTOSIS; ENDOCYTOSIS
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier51.44
Radius of gyration Rg (electron density) rg_electron51.08
Forward intensity I(0) i0707915000.00
Molecular weight molecular_weight210840.0 kDa
Excluded volume excluded_volume259260 ų
Envelope volume envelope_volume403780 ų
Hydration-shell volume shell_volume66148 ų
Envelope diameter envelope_diameter157.3
Shell Rg shell_rg55.29
Envelope Rg envelope_rg48.76
Shape Rg shape_rg51.04
Total Rg total_rg51.34
Total atoms total_atoms14763
Residues n_residues1919
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 dmax157.1
Rg (real space) rg_real51.32
Rg uncertainty (real space) rg_real_error1.41
I(0) (real space) i0_real7.0790e+08
I(0) uncertainty (real space) i0_real_error1.3510e+07
Rg (reciprocal space) rg_reciprocal51.53
I(0) (reciprocal space) i0_reciprocal708100000.0000
Solution quality estimate total_estimate0.6178
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary76.0
Skewness Skewness skewness0.046
Kurtosis Kurtosis kurtosis-0.772
Angular range angular_range— – 0.1550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26980000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.980; Stabil: 1.000; Sysdev: 0.029; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)