8xmp

Structure of CD163 in complex with Hb-Hp

Method: ELECTRON MICROSCOPY Dmax: 166.0 Å Quality: GOOD

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

Isoform 2 of Haptoglobin

Homo sapiens

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 Other combination Heteromer Protein × 6 其他Polymer 3 PDB declaration: hexameric(6) Consistent with protein copy count Chain 2; 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) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 CA CALCIUM ION × 23 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.11 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 1
Chains and sequence ranges Author chain 2; 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 Other combination Heteromer Protein × 6 其他Polymer 3 PDB declaration: hexameric(6) Consistent with protein copy count Chain D; UniProt 42–1050 Chain E; UniProt 42–1050 Chain F; UniProt 42–1050 Not recorded Isoform 2 of Haptoglobin × 1 (P00738) Hemoglobin subunit alpha × 1 (P69905) Hemoglobin subunit beta × 1 (P68871) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 CA CALCIUM ION × 23 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.11 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 2
Chains and sequence ranges Author chain D; PDBConstruct 1–1009; UniProt 42–1050 Author chain E; PDBConstruct 1–1009; UniProt 42–1050 Author chain F; PDBConstruct 1–1009; UniProt 42–1050

Hemoglobin subunit alpha

Homo sapiens

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 Other combination Heteromer Protein × 6 其他Polymer 3 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 1–142 Not recorded Isoform 2 of Haptoglobin × 1 (P00738) Scavenger receptor cysteine-rich type 1 protein M130 × 3 (Q86VB7) Hemoglobin subunit beta × 1 (P68871) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 CA CALCIUM ION × 23 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.11 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 3
Chains and sequence ranges Author chain C; PDBConstruct 1–142; UniProt 1–142

Hemoglobin subunit beta

Homo sapiens

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 Other combination Heteromer Protein × 6 其他Polymer 3 PDB declaration: hexameric(6) Consistent with protein copy count Chain G; UniProt 1–147 Not recorded Isoform 2 of Haptoglobin × 1 (P00738) Scavenger receptor cysteine-rich type 1 protein M130 × 3 (Q86VB7) Hemoglobin subunit alpha × 1 (P69905) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 CA CALCIUM ION × 23 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.11 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 4
Chains and sequence ranges Author chain G; PDBConstruct 1–147; UniProt 1–147

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 8xmp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8xmp
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8xmp
Deposition date deposition_date2023-12-27
Structure title titleStructure of CD163 in complex with Hb-Hp
Keywords keywordsscavenger receptor, ligand binding, ENDOCYTOSIS; ENDOCYTOSIS
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier54.03
Radius of gyration Rg (electron density) rg_electron53.42
Forward intensity I(0) i01742150000.00
Molecular weight molecular_weight328500.0 kDa
Excluded volume excluded_volume402060 ų
Envelope volume envelope_volume632460 ų
Hydration-shell volume shell_volume97895 ų
Envelope diameter envelope_diameter171.9
Shell Rg shell_rg59.53
Envelope Rg envelope_rg50.14
Shape Rg shape_rg53.40
Total Rg total_rg53.66
Total atoms total_atoms22949
Residues n_residues2972
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 dmax166.0
Rg (real space) rg_real53.67
Rg uncertainty (real space) rg_real_error1.28
I(0) (real space) i0_real1.7420e+09
I(0) uncertainty (real space) i0_real_error3.1410e+07
Rg (reciprocal space) rg_reciprocal54.31
I(0) (reciprocal space) i0_reciprocal1744000000.0000
Solution quality estimate total_estimate0.8701
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary80.1
Skewness Skewness skewness-0.089
Kurtosis Kurtosis kurtosis-0.489
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha66630000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.843

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

8. Citations (1)

9. Files and Curves (10)