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Entry
Database: PDB / ID: 3wcw
TitleThe structure of a deoxygenated 400 kda hemoglobin provides a more accurate description of the cooperative mechanism of giant hemoglobins: MG bound 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 / OXYGEN MOLECULE / Extracellular globin / Extracellular globin / Extracellular globin / Extracellular globin
Similarity search - Component
Biological speciesLamellibrachia satsuma (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 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 / pdbx_struct_special_symmetry / 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.occupancy / _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 / _pdbx_struct_special_symmetry.label_asym_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
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)137,51229
Polymers130,1388
Non-polymers7,37521
Water3,819212
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)412,53787
Polymers390,41324
Non-polymers22,12463
Water43224
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 area98130 Å2
ΔGint-675 kcal/mol
Surface area128400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.273, 109.273, 195.599
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-203-

MG

21A-342-

HOH

31A-343-

HOH

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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 , 4 types, 231 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-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: O2
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.52 %
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: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 11, 2010
RadiationMonochromator: Rotated-inclined double-crystal monochromator, Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 45675 / Num. obs: 45675 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 38.9 Å2 / Rsym value: 0.104 / Net I/σ(I): 15.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 4 / Num. unique all: 4577 / Rsym value: 0.395 / % possible all: 99.9

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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: 2.5→43.44 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2967154 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2299 5 %RANDOM
Rwork0.207 ---
obs0.207 45618 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.2298 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 42.0369 Å2
Baniso -1Baniso -2Baniso -3
1--2.93 Å20 Å20 Å2
2---2.93 Å20 Å2
3---5.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9108 0 505 212 9825
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_d17.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.022.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3 223 4.9 %
Rwork0.263 4363 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2hem_o2.paramhem_o2.top
X-RAY DIFFRACTION3mg_patch.parammg_patch.top
X-RAY DIFFRACTION4carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION5water_rep.paramwater.top

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