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- PDB-4mhj: Crystal structure of Fab H5M9 in complex with influenza virus hem... -

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Basic information

Entry
Database: PDB / ID: 4mhj
TitleCrystal structure of Fab H5M9 in complex with influenza virus hemagglutinin from A/goose/Guangdong/1/96 (H5N1)
Components
  • (H5M9 antibody, ...) x 2
  • (Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / H5N1 influenza virus / epitope / broadly neutralizing antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.98 Å
AuthorsZhu, X. / Wilson, I.A.
CitationJournal: J.Virol. / Year: 2013
Title: A Unique and Conserved Neutralization Epitope in H5N1 Influenza Viruses Identified by an Antibody against the A/Goose/Guangdong/1/96 Hemagglutinin.
Authors: Zhu, X. / Guo, Y.H. / Jiang, T. / Wang, Y.D. / Chan, K.H. / Li, X.F. / Yu, W. / McBride, R. / Paulson, J.C. / Yuen, K.Y. / Qin, C.F. / Che, X.Y. / Wilson, I.A.
History
DepositionAug 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
G: Hemagglutinin HA1 chain
M: Hemagglutinin HA1 chain
N: Hemagglutinin HA2 chain
O: Hemagglutinin HA1 chain
P: Hemagglutinin HA2 chain
S: Hemagglutinin HA1 chain
L: H5M9 antibody, light chain (kappa)
E: H5M9 antibody, light chain (kappa)
J: H5M9 antibody, light chain (kappa)
X: H5M9 antibody, light chain (kappa)
Q: H5M9 antibody, light chain (kappa)
V: H5M9 antibody, light chain (kappa)
I: Hemagglutinin HA2 chain
U: Hemagglutinin HA2 chain
H: H5M9 antibody, heavy chain (IgG1)
F: H5M9 antibody, heavy chain (IgG1)
K: H5M9 antibody, heavy chain (IgG1)
T: H5M9 antibody, heavy chain (IgG1)
R: H5M9 antibody, heavy chain (IgG1)
W: H5M9 antibody, heavy chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)646,82038
Polymers640,15224
Non-polymers6,66814
Water00
1
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
G: Hemagglutinin HA1 chain
L: H5M9 antibody, light chain (kappa)
E: H5M9 antibody, light chain (kappa)
J: H5M9 antibody, light chain (kappa)
I: Hemagglutinin HA2 chain
H: H5M9 antibody, heavy chain (IgG1)
F: H5M9 antibody, heavy chain (IgG1)
K: H5M9 antibody, heavy chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,51318
Polymers320,07612
Non-polymers3,4376
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
M: Hemagglutinin HA1 chain
N: Hemagglutinin HA2 chain
O: Hemagglutinin HA1 chain
P: Hemagglutinin HA2 chain
S: Hemagglutinin HA1 chain
X: H5M9 antibody, light chain (kappa)
Q: H5M9 antibody, light chain (kappa)
V: H5M9 antibody, light chain (kappa)
U: Hemagglutinin HA2 chain
T: H5M9 antibody, heavy chain (IgG1)
R: H5M9 antibody, heavy chain (IgG1)
W: H5M9 antibody, heavy chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,30720
Polymers320,07612
Non-polymers3,2318
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
G: Hemagglutinin HA1 chain
I: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,55712
Polymers176,1206
Non-polymers3,4376
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31780 Å2
ΔGint-74 kcal/mol
Surface area64350 Å2
MethodPISA
4
M: Hemagglutinin HA1 chain
N: Hemagglutinin HA2 chain
O: Hemagglutinin HA1 chain
P: Hemagglutinin HA2 chain
S: Hemagglutinin HA1 chain
U: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,35114
Polymers176,1206
Non-polymers3,2318
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32010 Å2
ΔGint-73 kcal/mol
Surface area63880 Å2
MethodPISA
5
L: H5M9 antibody, light chain (kappa)
H: H5M9 antibody, heavy chain (IgG1)


Theoretical massNumber of molelcules
Total (without water)47,9852
Polymers47,9852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-19 kcal/mol
Surface area19760 Å2
MethodPISA
6
E: H5M9 antibody, light chain (kappa)
F: H5M9 antibody, heavy chain (IgG1)


Theoretical massNumber of molelcules
Total (without water)47,9852
Polymers47,9852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-22 kcal/mol
Surface area19360 Å2
MethodPISA
7
J: H5M9 antibody, light chain (kappa)
K: H5M9 antibody, heavy chain (IgG1)


Theoretical massNumber of molelcules
Total (without water)47,9852
Polymers47,9852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-20 kcal/mol
Surface area19450 Å2
MethodPISA
8
X: H5M9 antibody, light chain (kappa)
T: H5M9 antibody, heavy chain (IgG1)


Theoretical massNumber of molelcules
Total (without water)47,9852
Polymers47,9852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-20 kcal/mol
Surface area19540 Å2
MethodPISA
9
Q: H5M9 antibody, light chain (kappa)
R: H5M9 antibody, heavy chain (IgG1)


Theoretical massNumber of molelcules
Total (without water)47,9852
Polymers47,9852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-21 kcal/mol
Surface area19330 Å2
MethodPISA
10
V: H5M9 antibody, light chain (kappa)
W: H5M9 antibody, heavy chain (IgG1)


Theoretical massNumber of molelcules
Total (without water)47,9852
Polymers47,9852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-20 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.552, 199.552, 466.886
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Hemagglutinin ... , 2 types, 12 molecules ACGMOSBDNPIU

#1: Protein
Hemagglutinin HA1 chain


Mass: 37812.707 Da / Num. of mol.: 6 / Fragment: receptor binding domain (UNP residues 17-346)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd / Gene: HA / Plasmid: pfastbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q9Q0U6
#2: Protein
Hemagglutinin HA2 chain


Mass: 20894.012 Da / Num. of mol.: 6 / Fragment: membrane fusion domain (UNP residues 347-521)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd / Gene: HA / Plasmid: pfastbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q9Q0U6

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Antibody , 2 types, 12 molecules LEJXQVHFKTRW

#3: Antibody
H5M9 antibody, light chain (kappa)


Mass: 24049.486 Da / Num. of mol.: 6 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
#4: Antibody
H5M9 antibody, heavy chain (IgG1)


Mass: 23935.797 Da / Num. of mol.: 6 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)

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Sugars , 6 types, 14 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c6-d1_d3-e1_d6-g1_e2-f1_g2-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#7: 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.: 2
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
#8: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#9: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#10: 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.: 6
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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.19 Å3/Da / Density % sol: 70.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 2% PEG400, 2.0 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 19, 2010
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 6.979→174.078 Å / Num. obs: 16538 / % possible obs: 93.3 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rsym value: 0.14 / Net I/σ(I): 12.9
Reflection shellResolution: 6.979→7.44 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.2 / Rsym value: 0.92 / % possible all: 64

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3GBM AND 4MHI

3gbm

4mhi


Resolution: 6.98→50.08 Å / Cor.coef. Fo:Fc: 0.759 / Cor.coef. Fo:Fc free: 0.792 / SU B: 0.008 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 4.762 / ESU R Free: 4.646 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.387 843 5.1 %RANDOM
Rwork0.377 ---
obs0.38 15673 92.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 89.86 Å2
Baniso -1Baniso -2Baniso -3
1-17.28 Å217.28 Å20 Å2
2--17.28 Å20 Å2
3----56.06 Å2
Refinement stepCycle: LAST / Resolution: 6.98→50.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43555 0 440 0 43995
LS refinement shellResolution: 6.98→7.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.609 43 -
Rwork0.553 661 -
obs--54.79 %

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