[English] 日本語
Yorodumi
- PDB-5vu4: Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza viru... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vu4
TitleCrystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin G225Q/L226A mutant in complex with 6'-SLN
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / Influenza A virus / hemagglutinin / mutant / receptor binding
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
Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
N-acetyl-alpha-neuraminic acid / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsWu, N.C. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI117675 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI114730 United States
CitationJournal: Cell Host Microbe / Year: 2017
Title: Diversity of Functionally Permissive Sequences in the Receptor-Binding Site of Influenza Hemagglutinin.
Authors: Wu, N.C. / Xie, J. / Zheng, T. / Nycholat, C.M. / Grande, G. / Paulson, J.C. / Lerner, R.A. / Wilson, I.A.
History
DepositionMay 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_validate_close_contact / 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_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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.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 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,22519
Polymers166,7316
Non-polymers5,49413
Water12,340685
1
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2816
Polymers55,5772
Non-polymers1,7044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-16 kcal/mol
Surface area23970 Å2
MethodPISA
2
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4436
Polymers55,5772
Non-polymers1,8664
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-11 kcal/mol
Surface area24090 Å2
MethodPISA
3
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5027
Polymers55,5772
Non-polymers1,9255
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-12 kcal/mol
Surface area24700 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39530 Å2
ΔGint-67 kcal/mol
Surface area56660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.344, 131.410, 72.345
Angle α, β, γ (deg.)90.00, 98.65, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13B
23D
14B
24F
15C
25E
16D
26F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROGLUGLUAA9 - 3253 - 319
21PROPROGLUGLUCC9 - 3253 - 319
12PROPROPROPROAA9 - 3243 - 318
22PROPROPROPROEE9 - 3243 - 318
13GLYGLYARGARGBB1 - 1701 - 170
23GLYGLYARGARGDD1 - 1701 - 170
14GLYGLYARGARGBB1 - 1701 - 170
24GLYGLYARGARGFF1 - 1701 - 170
15PROPROPROPROCC9 - 3243 - 318
25PROPROPROPROEE9 - 3243 - 318
16GLYGLYPHEPHEDD1 - 1711 - 171
26GLYGLYPHEPHEFF1 - 1711 - 171

NCS ensembles :
ID
6
1
2
3
4
5

-
Components

-
Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1 chain


Mass: 35535.945 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Hong Kong/1/1968 H3N2)
Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7
#2: Protein Hemagglutinin HA2 chain


Mass: 20041.131 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Hong Kong/1/1968 H3N2)
Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7

-
Sugars , 7 types, 13 molecules

#3: 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
#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 N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: 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
#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.: 4
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
#9: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 1 types, 685 molecules

#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 685 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate pH 6.5, 5% PEG 8000, and 38% 2-methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0331 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 91825 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 1 / Rpim(I) all: 0.03 / Rsym value: 0.08 / Net I/σ(I): 17.8
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 8243 / Rpim(I) all: 0.27 / Rsym value: 0.6 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000712data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FNK

4fnk


Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 10.835 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.181 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20765 4563 5 %RANDOM
Rwork0.18045 ---
obs0.1818 87261 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.453 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å2-0 Å2-0.85 Å2
2--0.13 Å2-0 Å2
3----0.8 Å2
Refinement stepCycle: 1 / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11526 0 364 685 12575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01912174
X-RAY DIFFRACTIONr_bond_other_d0.0040.0211155
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9716549
X-RAY DIFFRACTIONr_angle_other_deg1.124325740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89351463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54824.784579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.741151974
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5721570
X-RAY DIFFRACTIONr_chiral_restr0.0750.21868
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213749
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022806
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8023.0735870
X-RAY DIFFRACTIONr_mcbond_other0.8023.0735869
X-RAY DIFFRACTIONr_mcangle_it1.344.6067327
X-RAY DIFFRACTIONr_mcangle_other1.344.6077328
X-RAY DIFFRACTIONr_scbond_it1.3993.4186303
X-RAY DIFFRACTIONr_scbond_other1.3993.4186303
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2955.0819223
X-RAY DIFFRACTIONr_long_range_B_refined4.85730.02850374
X-RAY DIFFRACTIONr_long_range_B_other4.77129.8749851
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A368540.07
12C368540.07
21A367160.07
22E367160.07
31B182760.04
32D182760.04
41B181240.06
42F181240.06
51C367320.07
52E367320.07
61D182060.06
62F182060.06
LS refinement shellResolution: 2.248→2.306 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 312 -
Rwork0.261 5963 -
obs--92.24 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.81282.679-0.89238.34690.02971.5629-0.06090.3622-0.0385-0.54590.0784-0.36840.00860.318-0.01750.2486-0.10290.01280.41180.10510.1228.73118.642968.4598
20.2679-0.32660.15061.638-1.22671.9866-0.123-0.01140.02070.1039-0.0932-0.22640.10780.18690.21620.08440.0691-0.00060.2797-0.03010.152135.6453-29.8663110.7037
37.616-3.5595-4.49943.21312.81587.04290.08460.1158-0.0197-0.3483-0.24870.03750.0673-0.13510.16420.15960.036-0.03480.3538-0.03050.236725.3179-41.8352108.8834
41.2805-0.11550.58223.51341.01883.1657-0.0471-0.042-0.0003-0.0061-0.20250.11440.1348-0.21790.24970.0680.06930.0130.2609-0.02310.146329.5898-34.6916115.257
50.4095-0.260.24822.55-1.51331.3903-0.05720.1160.08640.0541-0.1182-0.4858-0.11680.30070.17540.066-0.03470.01470.26340.01670.147233.7309-4.198189.8896
610.72412.5895-2.27063.19570.65911.8056-0.35110.66660.4431-0.62280.11220.0897-0.0538-0.09830.23890.3333-0.10730.00630.29890.15250.207125.160524.669266.3219
72.1211.2965-1.80663.6964-4.07045.8524-0.10950.36590.368-0.02750.0847-0.1943-0.36510.21060.02470.2171-0.20810.02670.28090.11360.264432.538528.116276.4277
80.00940.4143-0.299223.7721-17.073512.2651-0.02340.01030.030.260.42990.516-0.1773-0.314-0.40650.4926-0.0222-0.07390.46190.02020.520828.323.333595.2558
90.26640.11180.00772.1141-0.64410.564-0.05780.16950.0601-0.12270.0256-0.24920.00050.14910.03230.1062-0.03210.03020.25490.0170.113821.6786-3.698585.669
101.73650.50690.73357.77080.91424.4159-0.11150.23830.3982-0.38550.1112-0.2381-0.43920.46350.00030.4193-0.15010.01260.24130.26930.472822.740341.638667.2799
116.3472-3.35411.00046.969-0.04745.4109-0.21160.14710.9428-0.00560.1428-0.3903-0.40740.36320.06870.5782-0.25250.01470.230.24470.683426.604649.502469.3529
120.73990.5423-0.37111.6532-0.82430.90910.0008-0.10720.09340.17120.04830.1037-0.01740.0531-0.04910.07640.02820.02020.1792-0.04140.0410.7956-13.9932112.009
131.987-0.10180.63151.08550.00912.1848-0.0473-0.038-0.2828-0.04440.0224-0.12630.33950.11110.02490.16780.05050.08150.11820.00910.092.1253-40.2795111.9184
140.76210.8853-0.54892.2815-1.07681.07830.0318-0.02370.27770.14080.11030.1666-0.19030.0404-0.14210.1259-0.00890.02840.1652-0.02790.1394.42522.3778104.1188
151.4891-1.7082-0.07713.0388-0.82671.11720.05760.00760.58820.27240.1916-0.0792-0.5274-0.0451-0.24920.3999-0.06730.02050.14720.16680.81898.595536.804487.7713
160.89940.99950.01419.54010.46310.8435-0.0410.13110.4716-0.00780.18740.6487-0.348-0.2835-0.14640.2680.06920.03230.25050.11010.4450.102827.635787.5326
170.33113.083-1.308229.6436-12.55165.3226-0.19580.0249-0.0052-1.19340.1105-0.3480.5114-0.09920.08530.5548-0.0404-0.08340.6080.1970.6211-0.970.209994.0994
180.51120.1148-0.08781.9918-0.86660.7491-0.02060.06420.29880.06440.08970.0623-0.16690.0958-0.06920.1419-0.03950.01560.18350.02980.212611.728510.879789.8194
193.9077-3.8775-4.06193.91963.18814.88780.15160.04090.3245-0.05610.0028-0.3076-0.7511-0.5092-0.15440.59070.0465-0.0210.12110.13780.71171.294951.4578.6689
203.5774-0.02540.85714.5235-3.21948.2130.08310.51170.64420.01260.25560.318-0.8277-0.5583-0.33870.58470.0971-0.00150.15810.25580.73171.254149.940970.8233
212.0141.02970.33585.6672-3.41935.9821-0.01020.38020.3849-0.44250.26420.65690.304-0.176-0.2540.0709-0.0058-0.11190.25660.17350.3205-1.407717.392868.168
221.53380.0488-0.08921.7891-0.91320.9838-0.11640.2179-0.5463-0.1762-0.0724-0.13710.26730.1340.18880.24860.04290.10890.2608-0.10830.2412.4191-43.62783.8096
2326.72973.8332-2.2795.56391.15375.25930.2107-0.382-0.22380.2488-0.2069-0.3866-0.05380.5091-0.00380.34020.0584-0.0950.34320.07390.15823.5633-45.096699.1114
246.07571.812-2.77641.9556-1.06123.0477-0.1958-0.3215-0.76950.0471-0.2531-0.27510.30490.46580.44890.24480.10490.0330.1762-0.01460.184814.778-47.765393.1087
250.865-0.32770.16761.9076-0.14260.5507-0.09570.33720.1244-0.1770.0144-0.03190.05290.13460.08130.14-0.03010.01340.34970.0180.03947.0457-15.507874.548
2627.47847.84043.41684.9888-2.03233.7141-0.3081-1.06471.23260.5789-0.7807-0.475-0.78610.3851.08880.7437-0.1571-0.18350.6857-0.03440.6798-14.679522.403666.3156
272.6652-0.96810.5412.7057-0.58161.2626-0.07550.5430.43-0.68210.15510.3094-0.05390.0456-0.07960.3125-0.1483-0.14440.41720.3130.26584.677719.872460.5013
282.18881.7052-1.742448.8297-18.47117.5532-0.2898-0.342-0.54840.6042-0.4834-1.3591-0.07780.3640.77320.4932-0.0162-0.02810.5821-0.00720.473115.0326-6.702271.7541
290.60.2905-0.11441.1034-0.27720.6782-0.08980.29870.3073-0.26140.14910.2505-0.0855-0.023-0.05930.188-0.0642-0.05830.32220.14240.1978.43169.748873.3954
307.44611.2929-2.27557.4152-1.95933.19860.01090.43020.4552-1.04870.2349-0.0044-0.62450.0033-0.24580.673-0.1125-0.06190.40330.36890.438512.526343.111952.2638
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 37
2X-RAY DIFFRACTION2A38 - 207
3X-RAY DIFFRACTION3A208 - 222
4X-RAY DIFFRACTION4A223 - 258
5X-RAY DIFFRACTION5A259 - 325
6X-RAY DIFFRACTION6B1 - 15
7X-RAY DIFFRACTION7B16 - 55
8X-RAY DIFFRACTION8B56 - 61
9X-RAY DIFFRACTION9B62 - 118
10X-RAY DIFFRACTION10B119 - 143
11X-RAY DIFFRACTION11B144 - 172
12X-RAY DIFFRACTION12C9 - 160
13X-RAY DIFFRACTION13C161 - 260
14X-RAY DIFFRACTION14C261 - 325
15X-RAY DIFFRACTION15D1 - 28
16X-RAY DIFFRACTION16D29 - 56
17X-RAY DIFFRACTION17D57 - 61
18X-RAY DIFFRACTION18D62 - 138
19X-RAY DIFFRACTION19D139 - 150
20X-RAY DIFFRACTION20D151 - 171
21X-RAY DIFFRACTION21E9 - 37
22X-RAY DIFFRACTION22E38 - 200
23X-RAY DIFFRACTION23E201 - 216
24X-RAY DIFFRACTION24E217 - 256
25X-RAY DIFFRACTION25E257 - 323
26X-RAY DIFFRACTION26E324 - 329
27X-RAY DIFFRACTION27F1 - 55
28X-RAY DIFFRACTION28F56 - 60
29X-RAY DIFFRACTION29F61 - 153
30X-RAY DIFFRACTION30F154 - 171

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more