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- PDB-4f4o: Structure of the Haptoglobin-Haemoglobin Complex -

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Basic information

Entry
Database: PDB / ID: 4f4o
TitleStructure of the Haptoglobin-Haemoglobin Complex
Components
  • (Hemoglobin subunit ...) x 2
  • Haptoglobin
KeywordsOXYGEN TRANSPORT/TRANSPORT PROTEIN / Globin Fold / Serine Protease Fold / Complement Control Protein / Haemoglobin scavenging / OXYGEN STORAGE-TRANSPORT complex / OXYGEN TRANSPORT-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


Scavenging of heme from plasma / : / acute inflammatory response / Neutrophil degranulation / zymogen activation / hemoglobin binding / immune system process / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex ...Scavenging of heme from plasma / : / acute inflammatory response / Neutrophil degranulation / zymogen activation / hemoglobin binding / immune system process / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / antioxidant activity / acute-phase response / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle / defense response to bacterium / iron ion binding / serine-type endopeptidase activity / heme binding / extracellular space / metal ion binding
Similarity search - Function
Haptoglobin / Complement Module, domain 1 / Complement Module; domain 1 / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin ...Haptoglobin / Complement Module, domain 1 / Complement Module; domain 1 / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain 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 / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Hemoglobin subunit alpha / Hemoglobin subunit beta / Haptoglobin
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAndersen, C.B.F. / Torvund-Jensen, M. / Nielsen, M.J. / Oliveira, C.L.P. / Hersleth, H.P. / Andersen, N.H. / Pedersen, J.S. / Andersen, G.R. / Moestrup, S.K.
CitationJournal: Nature / Year: 2012
Title: Structure of the haptoglobin-haemoglobin complex.
Authors: Andersen, C.B. / Torvund-Jensen, M. / Nielsen, M.J. / de Oliveira, C.L. / Hersleth, H.P. / Andersen, N.H. / Pedersen, J.S. / Andersen, G.R. / Moestrup, S.K.
History
DepositionMay 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / 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 / struct_asym / struct_conn / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity_src_nat.entity_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / entity_src_nat / Item: _entity.details

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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: Hemoglobin subunit alpha
E: Hemoglobin subunit beta
F: Haptoglobin
G: Hemoglobin subunit alpha
H: Hemoglobin subunit beta
I: Haptoglobin
J: Hemoglobin subunit alpha
K: Hemoglobin subunit beta
L: Haptoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)288,30943
Polymers278,60912
Non-polymers9,70031
Water00
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Haptoglobin
D: Hemoglobin subunit alpha
E: Hemoglobin subunit beta
F: Haptoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,36722
Polymers139,3056
Non-polymers5,06216
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12480 Å2
ΔGint-60 kcal/mol
Surface area50930 Å2
MethodPISA
2
G: Hemoglobin subunit alpha
H: Hemoglobin subunit beta
I: Haptoglobin
J: Hemoglobin subunit alpha
K: Hemoglobin subunit beta
L: Haptoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,94221
Polymers139,3056
Non-polymers4,63815
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12610 Å2
ΔGint-59 kcal/mol
Surface area50870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.880, 197.780, 322.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
13
23
14
24
15
25
35
45

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111Chain A
211Chain D
311Chain G
411Chain J
112Chain B
212Chain E
312Chain H
113Chain F and resid 38:97
213Chain L and resid 38:97
114Chain C and resid 38:97
214Chain I and resid 38:97
115Chain C and (resid 103:148 or resid 150:247 or resid 249:320 or resid 322:346)
215Chain F and (resid 103:148 or resid 150:247 or resid 249:320 or resid 322:346)
315Chain I and (resid 103:148 or resid 150:247 or resid 249:320 or resid 322:346)
415Chain L and (resid 103:148 or resid 150:247 or resid 249:320 or resid 322:346)

NCS ensembles :
ID
1
2
3
4
5
DetailsThe biological unit is composed of a Haptoglobin dimer binding two heamoglobin dimers.

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Components

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Hemoglobin subunit ... , 2 types, 8 molecules ADGJBEHK

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


Mass: 15064.144 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Purified from red blood cells / Source: (natural) Sus scrofa (pig) / References: UniProt: P01965
#2: Protein
Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 16058.360 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Purified from red blood cells / Source: (natural) Sus scrofa (pig) / References: UniProt: P02067

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Protein , 1 types, 4 molecules CFIL

#3: Protein
Haptoglobin / Haptoglobin alpha chain / Haptoglobin beta chain


Mass: 38529.773 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Purified from serum / Source: (natural) Sus scrofa (pig) / References: UniProt: Q8SPS7

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Sugars , 3 types, 15 molecules

#4: 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.: 3
Source method: isolated from a genetically manipulated source
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
#5: Polysaccharide
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#8: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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, 16 molecules

#6: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Details: Purified from serum
#7: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: O2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.17 Å3/Da / Density % sol: 70.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 18% PEG3350 10% Jeffamine M-600 200 mM Ammonium Citrate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 .0
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2011 / Details: Dynamically bendable mirror
RadiationMonochromator: Unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
201
ReflectionResolution: 2.9→20 Å / Num. all: 104337 / Num. obs: 103264 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.37 % / Rmerge(I) obs: 0.11 / Rsym value: 0.075 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.9-34.270.7242.030.635194.6
3-3.14.580.5173.050.489199.5
3.1-3.24.540.4183.890.393199.8
3.2-3.54.390.2556.340.231199.8
3.5-44.50.12412.660.107199.6
4-54.320.06721.530.058199.5

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QPW, 2QYO

1qpw

2qyo


Resolution: 2.9→20 Å / SU ML: 0.45 / σ(F): 2 / Phase error: 22.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 2251 2.18 %
Rwork0.2112 --
obs0.2116 103246 99.01 %
all-104337 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.012 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.3861 Å2-0 Å20 Å2
2---5.5029 Å20 Å2
3---3.1168 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18508 0 652 0 19160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01219756
X-RAY DIFFRACTIONf_angle_d1.6226875
X-RAY DIFFRACTIONf_dihedral_angle_d19.6076945
X-RAY DIFFRACTIONf_chiral_restr0.1222963
X-RAY DIFFRACTIONf_plane_restr0.0073382
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1109X-RAY DIFFRACTIONPOSITIONAL
12D1109X-RAY DIFFRACTIONPOSITIONAL0.071
13G1109X-RAY DIFFRACTIONPOSITIONAL0.057
14J1109X-RAY DIFFRACTIONPOSITIONAL0.051
21B1189X-RAY DIFFRACTIONPOSITIONAL
22E1189X-RAY DIFFRACTIONPOSITIONAL0.049
23H1189X-RAY DIFFRACTIONPOSITIONAL0.039
31F481X-RAY DIFFRACTIONPOSITIONAL
32L481X-RAY DIFFRACTIONPOSITIONAL0.049
41C481X-RAY DIFFRACTIONPOSITIONAL
42I481X-RAY DIFFRACTIONPOSITIONAL0.038
51C1886X-RAY DIFFRACTIONPOSITIONAL
52F1886X-RAY DIFFRACTIONPOSITIONAL0.115
53I1886X-RAY DIFFRACTIONPOSITIONAL0.133
54L1886X-RAY DIFFRACTIONPOSITIONAL0.158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9003-2.96340.37181280.36985774X-RAY DIFFRACTION92
2.9634-3.03230.38971400.35636304X-RAY DIFFRACTION99
3.0323-3.10810.3811360.32696215X-RAY DIFFRACTION100
3.1081-3.19220.36531410.31576334X-RAY DIFFRACTION100
3.1922-3.28610.32021380.28926270X-RAY DIFFRACTION100
3.2861-3.39210.30191400.26936268X-RAY DIFFRACTION100
3.3921-3.51330.26611410.26186342X-RAY DIFFRACTION100
3.5133-3.6540.23861410.24986302X-RAY DIFFRACTION100
3.654-3.82020.2571410.2256317X-RAY DIFFRACTION100
3.8202-4.02150.21711710.19586294X-RAY DIFFRACTION100
4.0215-4.27330.18231130.17866372X-RAY DIFFRACTION100
4.2733-4.60310.18361620.15586315X-RAY DIFFRACTION99
4.6031-5.06590.18261080.15946392X-RAY DIFFRACTION99
5.0659-5.79790.20741680.17576383X-RAY DIFFRACTION100
5.7979-7.3010.20831120.19526535X-RAY DIFFRACTION99
7.301-49.45220.18981710.18656578X-RAY DIFFRACTION98

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