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- PDB-4wjg: Structure of T. brucei haptoglobin-hemoglobin receptor binding to... -

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Basic information

Entry
Database: PDB / ID: 4wjg
TitleStructure of T. brucei haptoglobin-hemoglobin receptor binding to human haptoglobin-hemoglobin
Components
  • (Hemoglobin subunit ...) x 2
  • Haptoglobin-hemoglobin receptor
  • Haptoglobin
  • Iron-regulated surface determinant protein H
KeywordsENDOCYTOSIS / Trypanosome / Receptor
Function / homology
Function and homology information


negative regulation of hydrogen peroxide catabolic process / negative regulation of oxidoreductase activity / cell wall / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / immune system process ...negative regulation of hydrogen peroxide catabolic process / negative regulation of oxidoreductase activity / cell wall / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / immune system process / renal absorption / hemoglobin complex / antioxidant activity / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / acute-phase response / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / defense response / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / regulation of blood pressure / Chaperone Mediated Autophagy / specific granule lumen / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / defense response to bacterium / iron ion binding / serine-type endopeptidase activity / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol
Similarity search - Function
Ferritin - #80 / Iron-regulated surface determinant protein H / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / Complement Module, domain 1 / Complement Module; domain 1 ...Ferritin - #80 / Iron-regulated surface determinant protein H / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / Complement Module, domain 1 / Complement Module; domain 1 / YSIRK type signal peptide / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / YSIRK Gram-positive signal peptide / Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Ferritin / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Ribbon / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Up-down Bundle / Immunoglobulin-like / Beta Barrel / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Haptoglobin-hemoglobin receptor / Haptoglobin / Hemoglobin subunit beta / Hemoglobin subunit alpha / Iron-regulated surface determinant protein H
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria)
Trypanosoma brucei brucei (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsStoedkilde, K. / Torvund-Jensen, M. / Moestrup, S.K. / Andersen, C.B.F.
Funding support Denmark, 4items
OrganizationGrant numberCountry
The Lundbeck Foundation Denmark
The Novo Nordisk Foundation Denmark
The European Research Council Denmark
The Danish Council for Independent Research Denmark
CitationJournal: Nat Commun / Year: 2014
Title: Structural basis for trypanosomal haem acquisition and susceptibility to the host innate immune system.
Authors: Stdkilde, K. / Torvund-Jensen, M. / Moestrup, S.K. / Andersen, C.B.
History
DepositionSep 30, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen / entity_src_nat
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_nat.common_name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_src_gen / entity_src_nat / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity_src_nat.entity_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Haptoglobin
D: Iron-regulated surface determinant protein H
E: Haptoglobin-hemoglobin receptor
F: Hemoglobin subunit alpha
G: Hemoglobin subunit beta
H: Haptoglobin
I: Iron-regulated surface determinant protein H
J: Haptoglobin-hemoglobin receptor
K: Hemoglobin subunit alpha
L: Hemoglobin subunit beta
M: Haptoglobin
N: Iron-regulated surface determinant protein H
O: Haptoglobin-hemoglobin receptor
P: Hemoglobin subunit alpha
Q: Hemoglobin subunit beta
R: Haptoglobin
S: Iron-regulated surface determinant protein H
T: Haptoglobin-hemoglobin receptor
U: Hemoglobin subunit alpha
V: Hemoglobin subunit beta
W: Haptoglobin
X: Iron-regulated surface determinant protein H
Y: Haptoglobin-hemoglobin receptor
Z: Hemoglobin subunit alpha
1: Hemoglobin subunit beta
2: Haptoglobin
3: Iron-regulated surface determinant protein H
4: Haptoglobin-hemoglobin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)737,31787
Polymers720,20330
Non-polymers17,11457
Water0
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Haptoglobin
D: Iron-regulated surface determinant protein H
E: Haptoglobin-hemoglobin receptor
F: Hemoglobin subunit alpha
G: Hemoglobin subunit beta
H: Haptoglobin
I: Iron-regulated surface determinant protein H
J: Haptoglobin-hemoglobin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,70429
Polymers240,06810
Non-polymers5,63719
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: Hemoglobin subunit alpha
L: Hemoglobin subunit beta
M: Haptoglobin
N: Iron-regulated surface determinant protein H
O: Haptoglobin-hemoglobin receptor
P: Hemoglobin subunit alpha
Q: Hemoglobin subunit beta
R: Haptoglobin
S: Iron-regulated surface determinant protein H
T: Haptoglobin-hemoglobin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,12930
Polymers240,06810
Non-polymers6,06120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
U: Hemoglobin subunit alpha
V: Hemoglobin subunit beta
W: Haptoglobin
X: Iron-regulated surface determinant protein H
Y: Haptoglobin-hemoglobin receptor
Z: Hemoglobin subunit alpha
1: Hemoglobin subunit beta
2: Haptoglobin
3: Iron-regulated surface determinant protein H
4: Haptoglobin-hemoglobin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,48328
Polymers240,06810
Non-polymers5,41618
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.230, 140.950, 267.180
Angle α, β, γ (deg.)90.00, 98.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Hemoglobin subunit ... , 2 types, 12 molecules AFKPUZBGLQV1

#1: Protein
Hemoglobin subunit alpha / / Alpha-globin / Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein
Hemoglobin subunit beta / / Beta-globin / Hemoglobin beta chain


Mass: 15890.198 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871

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Protein , 3 types, 18 molecules CHMRW2DINSX3EJOTY4

#3: Protein
Haptoglobin / / Zonulin


Mass: 35267.066 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00738
#4: Protein
Iron-regulated surface determinant protein H / Haptoglobin receptor A / Staphylococcus aureus surface protein I


Mass: 16877.578 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: First NEAT domain
Source: (gene. exp.) Staphylococcus aureus subsp. aureus N315 (bacteria)
Gene: isdH, harA, sasI, SA1552 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta / References: UniProt: Q99TD3
#5: Protein
Haptoglobin-hemoglobin receptor


Mass: 36848.648 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: HpHbR / Plasmid: pPICz alpha A / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: I7BA80

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Sugars , 2 types, 33 molecules

#6: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: HpHbR / Plasmid: pPICz alpha A / Production host: Komagataella pastoris (fungus) / Strain (production host): X33
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#9: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 23
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: HpHbR / Plasmid: pPICz alpha A / Production host: Komagataella pastoris (fungus) / Strain (production host): X33
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 24 molecules

#7: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Source: (natural) Homo sapiens (human)
#8: Chemical
ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: O2 / Source: (natural) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.67 Å3/Da / Density % sol: 66.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 15% Polyethylene glycol (PEG) 1500, 0.1M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→29 Å / Num. obs: 184077 / % possible obs: 96.5 % / Redundancy: 2.8 % / Net I/σ(I): 7.2
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.44 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1702)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→29 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / Phase error: 37.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2709 1750 0.96 %
Rwork0.2551 --
obs0.2553 182377 96.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46650 0 1142 0 47792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01148930
X-RAY DIFFRACTIONf_angle_d1.55266526
X-RAY DIFFRACTIONf_dihedral_angle_d18.50717611
X-RAY DIFFRACTIONf_chiral_restr0.0657487
X-RAY DIFFRACTIONf_plane_restr0.0078482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.18370.4514980.407414029X-RAY DIFFRACTION97
3.1837-3.27730.35961940.375713830X-RAY DIFFRACTION97
3.2773-3.38290.40311000.340514050X-RAY DIFFRACTION97
3.3829-3.50360.31571350.315214025X-RAY DIFFRACTION97
3.5036-3.64360.32211590.296714066X-RAY DIFFRACTION97
3.6436-3.80910.2907970.278313977X-RAY DIFFRACTION96
3.8091-4.00950.27821960.265913685X-RAY DIFFRACTION95
4.0095-4.25990.2603970.24214118X-RAY DIFFRACTION97
4.2599-4.58770.2281980.223614132X-RAY DIFFRACTION97
4.5877-5.04720.24671920.220513943X-RAY DIFFRACTION96
5.0472-5.77250.26491000.23513967X-RAY DIFFRACTION96
5.7725-7.25380.24971970.232913884X-RAY DIFFRACTION96
7.2538-28.98410.1853870.182213511X-RAY DIFFRACTION91

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