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Basic information

Entry
Database: PDB / ID: 3wcu
TitleThe structure of a deoxygenated 400 kda hemoglobin provides a more accurate description of the cooperative mechanism of giant hemoglobins: Deoxygenated form
Components
  • A1 globin chain of giant V2 hemoglobin
  • A2 globin chain of giant V2 hemoglobin
  • B1 globin chain of giant V2 hemoglobin
  • B2 globin chain of giant V2 hemoglobin
KeywordsOXYGEN TRANSPORT / globin fold / oxygen binding / blood
Function / homology
Function and homology information


hemoglobin complex / oxygen carrier activity / oxygen binding / response to hypoxia / iron ion binding / heme binding / extracellular region
Similarity search - Function
Casein alpha/beta, conserved site / Caseins alpha/beta signature. / Globin, extracellular / Erythrocruorin / : / Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like ...Casein alpha/beta, conserved site / Caseins alpha/beta signature. / Globin, extracellular / Erythrocruorin / : / Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Extracellular globin / Extracellular globin / Extracellular globin / Extracellular globin
Similarity search - Component
Biological speciesLamellibrachia satsuma (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.9 Å
AuthorsNumoto, N. / Nakagawa, T. / Ohara, R. / Hasegawa, T. / Kita, A. / Yoshida, T. / Maruyama, T. / Imai, K. / Fukumori, Y. / Miki, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The structure of a deoxygenated 400 kDa haemoglobin reveals ternary- and quaternary-structural changes of giant haemoglobins
Authors: Numoto, N. / Nakagawa, T. / Ohara, R. / Hasegawa, T. / Kita, A. / Yoshida, T. / Maruyama, T. / Imai, K. / Fukumori, Y. / Miki, K.
History
DepositionJun 1, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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 / _chem_comp.name / _chem_comp.type / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 2.1Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: A1 globin chain of giant V2 hemoglobin
B: A2 globin chain of giant V2 hemoglobin
C: B2 globin chain of giant V2 hemoglobin
D: B1 globin chain of giant V2 hemoglobin
E: A1 globin chain of giant V2 hemoglobin
F: A2 globin chain of giant V2 hemoglobin
G: B2 globin chain of giant V2 hemoglobin
H: B1 globin chain of giant V2 hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,26420
Polymers130,1388
Non-polymers7,12612
Water00
1
A: A1 globin chain of giant V2 hemoglobin
B: A2 globin chain of giant V2 hemoglobin
C: B2 globin chain of giant V2 hemoglobin
D: B1 globin chain of giant V2 hemoglobin
E: A1 globin chain of giant V2 hemoglobin
F: A2 globin chain of giant V2 hemoglobin
G: B2 globin chain of giant V2 hemoglobin
H: B1 globin chain of giant V2 hemoglobin
hetero molecules

A: A1 globin chain of giant V2 hemoglobin
B: A2 globin chain of giant V2 hemoglobin
C: B2 globin chain of giant V2 hemoglobin
D: B1 globin chain of giant V2 hemoglobin
E: A1 globin chain of giant V2 hemoglobin
F: A2 globin chain of giant V2 hemoglobin
G: B2 globin chain of giant V2 hemoglobin
H: B1 globin chain of giant V2 hemoglobin
hetero molecules

A: A1 globin chain of giant V2 hemoglobin
B: A2 globin chain of giant V2 hemoglobin
C: B2 globin chain of giant V2 hemoglobin
D: B1 globin chain of giant V2 hemoglobin
E: A1 globin chain of giant V2 hemoglobin
F: A2 globin chain of giant V2 hemoglobin
G: B2 globin chain of giant V2 hemoglobin
H: B1 globin chain of giant V2 hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)411,79160
Polymers390,41324
Non-polymers21,37836
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area98420 Å2
ΔGint-748 kcal/mol
Surface area125830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.872, 108.872, 195.157
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein A1 globin chain of giant V2 hemoglobin


Mass: 16368.704 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lamellibrachia satsuma (invertebrata) / Tissue: blood / References: UniProt: S0BBU7
#2: Protein A2 globin chain of giant V2 hemoglobin


Mass: 15951.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lamellibrachia satsuma (invertebrata) / Tissue: blood / References: UniProt: S0BBR6
#3: Protein B2 globin chain of giant V2 hemoglobin


Mass: 16519.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lamellibrachia satsuma (invertebrata) / Tissue: blood / References: UniProt: S0BCU7
#4: Protein B1 globin chain of giant V2 hemoglobin


Mass: 16228.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lamellibrachia satsuma (invertebrata) / Tissue: blood / References: UniProt: S0BAP9

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Sugars , 1 types, 2 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-2-2-3/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 10 molecules

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


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 13-18% PEG 3350, 0-5mM Ca acetate/Mg acetate, 100mM HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jul 6, 2009
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 28054 / Num. obs: 28054 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 95.4 Å2 / Rsym value: 0.096 / Net I/σ(I): 13.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 2864 / Rsym value: 0.503 / % possible all: 98.8

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Processing

Software
NameVersionClassification
BSSdata collection
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
CNS1.2phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3WCT

3wct


Resolution: 2.9→42.45 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 2559595 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL USED. The model was constructed only one copy of each of the four subunits and refined by applying strict NCS constraints (i.e., the chains A, B, C, and D are identical to ...Details: BULK SOLVENT MODEL USED. The model was constructed only one copy of each of the four subunits and refined by applying strict NCS constraints (i.e., the chains A, B, C, and D are identical to the chains E, F, G, and H, respectively).
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1436 5.1 %RANDOM
Rwork0.246 ---
obs0.246 27985 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.1643 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 239.09 Å2 / Biso mean: 70.7541 Å2 / Biso min: 10.85 Å2
Baniso -1Baniso -2Baniso -3
1--5.25 Å20 Å20 Å2
2---5.25 Å20 Å2
3---10.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.8 Å0.63 Å
Refinement stepCycle: LAST / Resolution: 2.9→42.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9138 0 488 0 9626
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.439 166 5.8 %
Rwork0.359 2682 -
all-2848 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2hem_o2.paramhem_o2.top
X-RAY DIFFRACTION3ca.paamrca.top
X-RAY DIFFRACTION4carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION5water_rep.paramwater.top

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