5hu6

Structure of the T. brucei haptoglobin-haemoglobin receptor bound to human haptolgobin-haemoglobin

Method: X-RAY DIFFRACTION Dmax: 116.0 Å Quality: GOOD

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

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 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 2–142 Not recorded Hemoglobin subunit beta × 1 (P68871) Haptoglobin × 1 (P00738) Haptoglobin-hemoglobin receptor × 1 (I7B1A7) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;12.5% v/v MPD, 0.03 M NaBr, 0.03M NaI, 0.03M NaF, 0.1 M MES/imidazole pH 6.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350 Resolution 2.90 Å R-free 0.226

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 1–141; UniProt 2–142

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 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 3–143 Not recorded Hemoglobin subunit alpha × 1 (P69905) Haptoglobin × 1 (P00738) Haptoglobin-hemoglobin receptor × 1 (I7B1A7) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;12.5% v/v MPD, 0.03 M NaBr, 0.03M NaI, 0.03M NaF, 0.1 M MES/imidazole pH 6.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350 Resolution 2.90 Å R-free 0.226

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 1–141; UniProt 3–143

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 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 148–406 Not recorded Hemoglobin subunit alpha × 1 (P69905) Hemoglobin subunit beta × 1 (P68871) Haptoglobin-hemoglobin receptor × 1 (I7B1A7) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;12.5% v/v MPD, 0.03 M NaBr, 0.03M NaI, 0.03M NaF, 0.1 M MES/imidazole pH 6.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350 Resolution 2.90 Å R-free 0.226

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
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–259; UniProt 148–406

Haptoglobin-hemoglobin receptor

Trypanosoma brucei brucei

UniProt I7B1A7

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 38–297 Not recorded Hemoglobin subunit alpha × 1 (P69905) Hemoglobin subunit beta × 1 (P68871) Haptoglobin × 1 (P00738) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;12.5% v/v MPD, 0.03 M NaBr, 0.03M NaI, 0.03M NaF, 0.1 M MES/imidazole pH 6.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350 Resolution 2.90 Å R-free 0.226

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name I7B1A7_TRYBB
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–260; UniProt 38–297

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 5hu6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5hu6
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id5hu6
Deposition date deposition_date2016-01-27
Structure title titleStructure of the T. brucei haptoglobin-haemoglobin receptor bound to human haptolgobin-haemoglobin
Keywords keywordsTrypanosome haptoglobin-haemoglobin, Transport Protein; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.54
Radius of gyration Rg (electron density) rg_electron31.00
Forward intensity I(0) i0119437000.00
Molecular weight molecular_weight86839.0 kDa
Excluded volume excluded_volume108850 ų
Envelope volume envelope_volume137770 ų
Hydration-shell volume shell_volume38167 ų
Envelope diameter envelope_diameter123.2
Shell Rg shell_rg36.66
Envelope Rg envelope_rg31.72
Shape Rg shape_rg30.96
Total Rg total_rg31.64
Total atoms total_atoms6116
Residues n_residues784
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 dmax116.0
Rg (real space) rg_real31.65
Rg uncertainty (real space) rg_real_error1.21
I(0) (real space) i0_real1.1940e+08
I(0) uncertainty (real space) i0_real_error2.1070e+06
Rg (reciprocal space) rg_reciprocal31.60
I(0) (reciprocal space) i0_reciprocal119400000.0000
Solution quality estimate total_estimate0.8402
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.1
Skewness Skewness skewness0.505
Kurtosis Kurtosis kurtosis0.075
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22150000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.669; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.942; Smooth: 0.968

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5hu6a_
Class classa — All alpha proteins
Fold Fold folda.1 — Globin-like
Superfamily Superfamily superfamilya.1.1 — Globin-like
Family Family familya.1.1.2 — Globins
Domain ID domain_idd5hu6b_
Class classa — All alpha proteins
Fold Fold folda.1 — Globin-like
Superfamily Superfamily superfamilya.1.1 — Globin-like
Family Family familya.1.1.2 — Globins

CATH v4.4 (3 domains)

Domain ID domain_id5hu6A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5hu6B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5hu6D00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily80

8. Citations (1)

9. Files and Curves (10)