[English] 日本語
Yorodumi
- PDB-7jpd: Crystal structure of the trimeric full length mature hemagglutini... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jpd
TitleCrystal structure of the trimeric full length mature hemagglutinin from influenza A virus A/Fort Monmouth/1/1947
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / National Institutes of Allergy and Infectious Diseases / NIAID / flu / seasonal flu / vaccine / HA / antigen / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / host cell surface receptor binding / apical plasma membrane / 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
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
IODIDE ION / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Sci Rep / Year: 2023
Title: Structural characterisation of hemagglutinin from seven Influenza A H1N1 strains reveal diversity in the C05 antibody recognition site.
Authors: Ghafoori, S.M. / Petersen, G.F. / Conrady, D.G. / Calhoun, B.M. / Stigliano, M.Z.Z. / Baydo, R.O. / Grice, R. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E. / Forwood, J.K.
History
DepositionAug 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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_asym_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 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin HA1 chain
a: Hemagglutinin HA2 chain
B: Hemagglutinin HA1 chain
b: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
c: Hemagglutinin HA2 chain
D: Hemagglutinin HA1 chain
d: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
e: Hemagglutinin HA2 chain
F: Hemagglutinin HA1 chain
f: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,215111
Polymers338,29912
Non-polymers18,91699
Water3,063170
1
A: Hemagglutinin HA1 chain
a: Hemagglutinin HA2 chain
D: Hemagglutinin HA1 chain
d: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
e: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,85457
Polymers169,1496
Non-polymers9,70451
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hemagglutinin HA1 chain
b: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
c: Hemagglutinin HA2 chain
F: Hemagglutinin HA1 chain
f: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,36154
Polymers169,1496
Non-polymers9,21248
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.790, 142.360, 234.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 12 or (resid 13...
21(chain B and (resid 2 through 12 or (resid 13...
31(chain C and (resid 2 through 12 or (resid 13...
41(chain D and (resid 2 through 23 or (resid 24...
51(chain E and (resid 2 through 12 or (resid 13...
61(chain F and (resid 2 through 12 or (resid 13...
12chain H
22chain I
32chain K
42chain M
52chain O
62chain Q
13chain J
23chain L
33chain N
43chain P

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERASNASN(chain A and (resid 2 through 12 or (resid 13...AA2 - 122 - 12
121ASNASNASNASN(chain A and (resid 2 through 12 or (resid 13...AA1313
131SERSERPROPRO(chain A and (resid 2 through 12 or (resid 13...A - aA - B2 - 4892 - 160
141SERSERPROPRO(chain A and (resid 2 through 12 or (resid 13...A - aA - B2 - 4892 - 160
151SERSERPROPRO(chain A and (resid 2 through 12 or (resid 13...A - aA - B2 - 4892 - 160
161SERSERPROPRO(chain A and (resid 2 through 12 or (resid 13...A - aA - B2 - 4892 - 160
211SERSERASNASN(chain B and (resid 2 through 12 or (resid 13...BC2 - 122 - 12
221ASNASNASNASN(chain B and (resid 2 through 12 or (resid 13...BC1313
231SERSERPROPRO(chain B and (resid 2 through 12 or (resid 13...B - bC - D2 - 4892 - 160
241SERSERPROPRO(chain B and (resid 2 through 12 or (resid 13...B - bC - D2 - 4892 - 160
251SERSERPROPRO(chain B and (resid 2 through 12 or (resid 13...B - bC - D2 - 4892 - 160
261SERSERPROPRO(chain B and (resid 2 through 12 or (resid 13...B - bC - D2 - 4892 - 160
311SERSERASNASN(chain C and (resid 2 through 12 or (resid 13...CE2 - 122 - 12
321ASNASNASNASN(chain C and (resid 2 through 12 or (resid 13...CE1313
331SERSERPROPRO(chain C and (resid 2 through 12 or (resid 13...C - cE - F2 - 4892 - 160
341SERSERPROPRO(chain C and (resid 2 through 12 or (resid 13...C - cE - F2 - 4892 - 160
351SERSERPROPRO(chain C and (resid 2 through 12 or (resid 13...C - cE - F2 - 4892 - 160
411SERSERGLUGLU(chain D and (resid 2 through 23 or (resid 24...DG2 - 232 - 23
421LYSLYSLYSLYS(chain D and (resid 2 through 23 or (resid 24...DG2424
431SERSERPROPRO(chain D and (resid 2 through 23 or (resid 24...D - dG - H2 - 4892 - 160
441SERSERPROPRO(chain D and (resid 2 through 23 or (resid 24...D - dG - H2 - 4892 - 160
451SERSERPROPRO(chain D and (resid 2 through 23 or (resid 24...D - dG - H2 - 4892 - 160
511SERSERASNASN(chain E and (resid 2 through 12 or (resid 13...EI2 - 122 - 12
521ASNASNASNASN(chain E and (resid 2 through 12 or (resid 13...EI1313
531SERSERPROPRO(chain E and (resid 2 through 12 or (resid 13...E - eI - J2 - 4892 - 160
541SERSERPROPRO(chain E and (resid 2 through 12 or (resid 13...E - eI - J2 - 4892 - 160
551SERSERPROPRO(chain E and (resid 2 through 12 or (resid 13...E - eI - J2 - 4892 - 160
611SERSERASNASN(chain F and (resid 2 through 12 or (resid 13...FK2 - 122 - 12
621ASNASNASNASN(chain F and (resid 2 through 12 or (resid 13...FK1313
631SERSERPROPRO(chain F and (resid 2 through 12 or (resid 13...F - fK - L2 - 4892 - 160
112NAGNAGNAGNAGchain HHN1 - 2
212NAGNAGNAGNAGchain IIO1 - 2
312NAGNAGNAGNAGchain KKQ1 - 2
412NAGNAGNAGNAGchain MMS1 - 2
512NAGNAGNAGNAGchain OOU1 - 2
612NAGNAGNAGNAGchain QQW1 - 2
113NAGNAGMANMANchain JJP1 - 5
213NAGNAGMANMANchain LLR1 - 5
313NAGNAGMANMANchain NNT1 - 5
413NAGNAGMANMANchain PPV1 - 5

NCS ensembles :
ID
1
2
3

-
Components

-
Hemagglutinin ... , 2 types, 12 molecules ABCDEFabcdef

#1: Protein
Hemagglutinin HA1 chain


Mass: 36860.414 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Fort Monmouth/1/1947(H1N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q20MG8
#2: Protein
Hemagglutinin HA2 chain


Mass: 19522.717 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Fort Monmouth/1/1947(H1N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q20MG8

-
Sugars , 4 types, 22 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-ROHGlycam 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
[][D-1-deoxy-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.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Polysaccharide
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-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: 910.823 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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.: 11
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

-
Non-polymers , 3 types, 247 molecules

#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 76 / Source method: obtained synthetically / Formula: I
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: InvbN.18715.a.KN11.PD38312 at 9.84 mg/mL against MCSG1 screen condition D11: 0.2 M sodium iodide, 20% PEG 3350 supplemented with 20% ethylene glycol as cryo-protectant; crystal tracking ID ...Details: InvbN.18715.a.KN11.PD38312 at 9.84 mg/mL against MCSG1 screen condition D11: 0.2 M sodium iodide, 20% PEG 3350 supplemented with 20% ethylene glycol as cryo-protectant; crystal tracking ID 301393d11, unique puck ID umg7-8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→48.85 Å / Num. obs: 91660 / % possible obs: 98.2 % / Redundancy: 6.256 % / Biso Wilson estimate: 57.51 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.145 / Rrim(I) all: 0.159 / Χ2: 1.026 / Net I/σ(I): 9.41 / Num. measured all: 573436 / Scaling rejects: 10124
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.95-3.036.9670.828247409680568050.7150.894100
3.03-3.116.8810.6132.7445750665166490.8410.663100
3.11-3.26.7390.5273.2443613647564720.8710.571100
3.2-3.36.4660.4583.7840809632263110.9020.49899.8
3.3-3.416.2660.3864.3737716609660190.940.42298.7
3.41-3.535.6640.2966.0232292589357010.9610.32896.7
3.53-3.666.1890.2128.0333100573953480.9770.23493.2
3.66-3.816.4140.218.3233034548251500.9730.2393.9
3.81-3.985.6640.179.826821527147350.9820.18989.8
3.98-4.176.3120.13211.9231808505150390.9890.14499.8
4.17-4.45.8150.11612.7328028483448200.990.12899.7
4.4-4.665.8140.09714.5726460456145510.9920.10799.8
4.66-4.996.2540.09415.2826898431043010.9930.10399.8
4.99-5.396.3010.09415.3225124399239870.9930.10399.9
5.39-5.96.2060.09715.0222986371237040.9930.10699.8
5.9-6.65.770.09414.5619468338633740.9930.10499.6
6.6-7.626.0160.07816.9117951299229840.9950.08699.7
7.62-9.336.2430.05720.5215927255625510.9980.06299.8
9.33-13.195.6570.04721.811411202220170.9980.05299.8
13.19-48.855.9820.03823.466831117311420.9990.04197.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIXdev-4274refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vli

5vli


Resolution: 2.95→48.85 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 27.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2864 4458 4.87 %
Rwork0.2538 87102 -
obs0.2554 91560 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.43 Å2 / Biso mean: 53.3845 Å2 / Biso min: 28.13 Å2
Refinement stepCycle: final / Resolution: 2.95→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22128 0 685 170 22983
Biso mean--63.46 48.9 -
Num. residues----2895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423256
X-RAY DIFFRACTIONf_angle_d0.67131649
X-RAY DIFFRACTIONf_dihedral_angle_d18.5968244
X-RAY DIFFRACTIONf_chiral_restr0.0453584
X-RAY DIFFRACTIONf_plane_restr0.0054084
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A12909X-RAY DIFFRACTION8.29TORSIONAL
12B12909X-RAY DIFFRACTION8.29TORSIONAL
13C12909X-RAY DIFFRACTION8.29TORSIONAL
14D12909X-RAY DIFFRACTION8.29TORSIONAL
15E12909X-RAY DIFFRACTION8.29TORSIONAL
16F12909X-RAY DIFFRACTION8.29TORSIONAL
21H72X-RAY DIFFRACTION8.29TORSIONAL
22I72X-RAY DIFFRACTION8.29TORSIONAL
23K72X-RAY DIFFRACTION8.29TORSIONAL
24M72X-RAY DIFFRACTION8.29TORSIONAL
25O72X-RAY DIFFRACTION8.29TORSIONAL
26Q72X-RAY DIFFRACTION8.29TORSIONAL
31J168X-RAY DIFFRACTION8.29TORSIONAL
32L168X-RAY DIFFRACTION8.29TORSIONAL
33N168X-RAY DIFFRACTION8.29TORSIONAL
34P168X-RAY DIFFRACTION8.29TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-2.980.39951700.356629083078100
2.98-3.020.39921470.358329173064100
3.02-3.060.33491640.315528873051100
3.06-3.090.31811600.295729183078100
3.09-3.130.27271580.28329293087100
3.13-3.180.27861410.283129163057100
3.18-3.220.30781450.276729413086100
3.22-3.270.33141440.275229183062100
3.27-3.320.28781430.271629233066100
3.32-3.380.31071350.262829453080100
3.38-3.430.48551410.40382752289394
3.44-3.50.3711560.31462842299897
3.5-3.560.29771540.265129453099100
3.56-3.640.32351480.29812566271489
3.64-3.720.49291050.44592602270787
3.72-3.80.28071590.260929373096100
3.8-3.90.38281260.36252660278690
3.9-40.32121200.2642732285292
4-4.120.22441550.215729423097100
4.12-4.250.26651490.204629323081100
4.25-4.410.20941570.200529753132100
4.41-4.580.21341620.188629073069100
4.58-4.790.23081610.183629483109100
4.79-5.040.24771610.201729453106100
5.04-5.360.24491280.200130193147100
5.36-5.770.24421710.21129593130100
5.77-6.350.22961500.214230003150100
6.35-7.270.24141550.22130063161100
7.27-9.150.23031440.205330573201100
9.15-48.850.28311490.23583174332399
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)
10.94120.50262.15831.30481.56085.04480.3795-0.0221-0.1174-0.1172-0.12060.20.8931-0.049-0.0650.6312-0.06950.01360.3276-0.01540.419510.172-0.92917.035
21.10490.20771.19631.20261.987.9716-0.1464-0.2952-0.04440.3221-0.0875-0.06470.5641-0.0350.14430.4870.05960.02940.36190.04740.431525.16511.64151.607
32.24710.0119-0.68162.42770.24864.1128-0.0735-0.3889-0.05230.38530.0091-0.35410.39470.41270.06430.3380.0533-0.05310.3579-0.00220.407231.79120.35765.641
42.03781.00091.64251.65621.99864.7535-0.08880.0344-0.3075-0.35130.1425-0.2257-0.20260.04410.01040.36080.0863-0.04370.23030.00570.462529.66813.2147.382
50.70560.32860.9130.70160.51833.61650.2150.2216-0.2259-0.28130.05450.05370.4643-0.3804-0.18110.5521-0.0106-0.04410.3681-0.0220.44527.507-1.1395.64
60.5790.03640.61921.62281.78334.64240.02180.1373-0.1932-0.3701-0.06620.0426-0.0843-0.1303-0.11830.4411-0.0430.00690.3417-0.03690.41929.1556.913.776
70.85230.349-1.09660.5229-0.23561.77920.1974-0.04680.19320.1151-0.0663-0.0258-0.7945-0.0027-0.1610.65660.00890.04880.3451-0.03910.396654.294-0.78422.229
81.14740.6467-0.24421.8734-1.43474.2335-0.0109-0.32080.05890.4634-0.10690.088-0.40010.23380.04540.5560.06720.05050.3254-0.06840.35733.873-16.7159.537
92.30580.34410.00011.2894-1.36732.0937-0.0291-0.2887-0.07340.31280.03780.1174-0.2785-0.158-0.07660.39840.08170.06240.2715-0.02760.330733.735-27.07460.581
102.1589-0.6541-0.68381.6672-0.08642.19790.06040.28950.1652-0.06240.0547-0.1538-0.6323-0.225-0.20260.42510.0344-0.05260.36980.04820.43247.318-4.2632.551
110.88310.0019-0.37851.5586-0.75142.30260.11280.24980.2296-0.29910.0824-0.0284-0.3962-0.0583-0.13260.5349-0.02590.08280.33070.00930.392358.681-2.9135.088
121.41821.6356-2.59182.7332-3.46525.0888-0.21480.2881-0.0358-0.35150.36050.19320.507-0.4802-0.10660.4098-0.0774-0.00770.44210.01720.404340.289-37.83515.266
132.01590.33430.0852.0086-0.67953.5662-0.02730.0704-0.13690.04650.083-0.09730.171-0.1837-0.0320.3577-0.01020.0520.2219-0.03450.409136.436-53.7945.844
141.08150.6559-2.39050.6038-1.79368.5963-0.07480.0381-0.0024-0.17390.11070.01810.15130.2954-0.02760.4217-0.05240.02550.4287-0.04370.332755.697-22.722-4.109
150.55790.67891.84831.19652.73795.1875-0.24160.4410.161-0.30540.5221-0.0466-0.76661.054-0.19910.6102-0.22870.07440.5818-0.01320.481726.72837.36517.072
162.0788-0.23470.53092.30040.92083.6082-0.0650.08130.3098-0.00180.1031-0.1545-0.26080.3614-0.01150.3983-0.07620.05480.2354-0.0410.432630.89351.63553.147
170.4479-0.37160.36282.22421.89532.71290.00160.23090.2503-0.56550.1243-0.0856-0.26690.0942-0.17010.5614-0.1950.05450.35310.05740.527525.14449.38136.38
180.5897-0.13870.47110.14750.11354.1506-0.07310.1742-0.0373-0.16940.05590.046-0.2429-0.05930.04170.4122-0.0687-0.00260.3810.00180.336311.524.283-4.044
190.45120.52751.21560.77781.17832.4733-0.2153-0.07530.0446-0.1605-0.37910.4133-0.4511-0.96730.5680.43550.0411-0.1440.6156-0.02620.5616-12.3727.71213.967
201.24131.27372.34684.89684.27996.7975-0.1059-0.18690.3732-0.3976-0.37730.9908-0.593-0.30130.40490.3620.12640.0760.52380.00490.5168-5.14138.34752.261
211.91230.82770.58492.6280.15882.503-0.0193-0.21890.090.2197-0.01730.1607-0.063-0.18230.07490.31020.04810.08230.39010.01140.35753.41437.39166.466
220.0454-0.00590.1220.01330.12525.0584-0.14880.054-0.11070.2710.00870.35420.1378-0.06070.2090.2941-0.0206-0.00630.62290.02350.5707-8.58329.82936.85
231.17440.54321.64041.12262.29925.008-0.3174-0.09010.2347-0.1281-0.07250.5265-0.6675-0.79010.35930.2625-0.0337-0.01580.49230.01740.4173-5.95225.7549.889
241.93171.44592.78472.49741.77644.0488-0.145-0.33970.46810.3581-0.27731.207-0.0499-1.12520.70460.47380.0158-0.20610.8551-0.13380.6628-21.41515.274-11.177
252.91382.72874.3613.0314.5068.81780.3101-0.30710.00680.4198-0.41320.02430.9325-0.48050.14490.4035-0.0160.06890.3417-0.06240.3467-3.55820.10321.588
262.37511.70483.29292.07392.97166.7872-0.27440.4460.0168-0.3340.14450.3598-0.02080.04760.10060.3946-0.1215-0.07310.5193-0.06610.464-6.65915.522-2.003
270.5490.1987-0.90540.8237-1.71755.1959-0.1349-0.1027-0.1193-0.1578-0.2469-0.43170.31030.85110.53230.38560.07330.09520.50180.04820.601275.292-32.92129.044
282.58860.5956-0.52032.19850.47362.5027-0.0961-0.4224-0.14680.4588-0.0485-0.1420.15260.16870.17810.44510.1447-0.03970.42360.04090.366261.533-41.81765.195
290.78210.51150.09860.6425-0.84414.127-0.19220.10610.2203-0.0259-0.2321-0.3158-0.26550.59670.39980.46690.1335-0.00940.52220.04880.532268.972-32.88451.894
301.39750.764-1.41821.8305-1.19212.57190.0130.18280.1353-0.18210.1259-0.3552-0.1610.2821-0.06850.3486-0.11730.12130.5072-0.04470.554774.863-17.8435.378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:58 )A2 - 58
2X-RAY DIFFRACTION2( CHAIN A AND RESID 59:109 )A59 - 109
3X-RAY DIFFRACTION3( CHAIN A AND RESID 110:236 )A110 - 236
4X-RAY DIFFRACTION4( CHAIN A AND RESID 237:288 )A237 - 288
5X-RAY DIFFRACTION5( CHAIN A AND RESID 289:324 ) OR ( CHAIN a AND RESID 330:366 )A289 - 324
6X-RAY DIFFRACTION5( CHAIN A AND RESID 289:324 ) OR ( CHAIN a AND RESID 330:366 )a330 - 366
7X-RAY DIFFRACTION6( CHAIN a AND RESID 367:489 )a367 - 489
8X-RAY DIFFRACTION7( CHAIN B AND RESID 2:64 )B2 - 64
9X-RAY DIFFRACTION8( CHAIN B AND RESID 65:162 )B65 - 162
10X-RAY DIFFRACTION9( CHAIN B AND RESID 163:269 )B163 - 269
11X-RAY DIFFRACTION10( CHAIN B AND RESID 270:298 )B270 - 298
12X-RAY DIFFRACTION11( CHAIN B AND RESID 299:324 ) OR ( CHAIN b AND RESID 330:489 )B299 - 324
13X-RAY DIFFRACTION11( CHAIN B AND RESID 299:324 ) OR ( CHAIN b AND RESID 330:489 )b330 - 489
14X-RAY DIFFRACTION12( CHAIN C AND RESID 2:99 )C2 - 99
15X-RAY DIFFRACTION13( CHAIN C AND RESID 100:288 )C100 - 288
16X-RAY DIFFRACTION14( CHAIN C AND RESID 289:324 ) OR ( CHAIN c AND RESID 330:489 )C289 - 324
17X-RAY DIFFRACTION14( CHAIN C AND RESID 289:324 ) OR ( CHAIN c AND RESID 330:489 )c330 - 489
18X-RAY DIFFRACTION15( CHAIN D AND RESID 2:99 )D2 - 99
19X-RAY DIFFRACTION16( CHAIN D AND RESID 100:236 )D100 - 236
20X-RAY DIFFRACTION17( CHAIN D AND RESID 237:288 )D237 - 288
21X-RAY DIFFRACTION18( CHAIN D AND RESID 289:324 ) OR ( CHAIN d AND RESID 330:489 )D289 - 324
22X-RAY DIFFRACTION18( CHAIN D AND RESID 289:324 ) OR ( CHAIN d AND RESID 330:489 )d330 - 489
23X-RAY DIFFRACTION19( CHAIN E AND RESID 2:58 )E2 - 58
24X-RAY DIFFRACTION20( CHAIN E AND RESID 59:99 )E59 - 99
25X-RAY DIFFRACTION21( CHAIN E AND RESID 100:254 )E100 - 254
26X-RAY DIFFRACTION22( CHAIN E AND RESID 255:298 )E255 - 298
27X-RAY DIFFRACTION23( CHAIN E AND RESID 299:324 ) OR ( CHAIN e AND RESID 330:337 )E299 - 324
28X-RAY DIFFRACTION23( CHAIN E AND RESID 299:324 ) OR ( CHAIN e AND RESID 330:337 )e330 - 337
29X-RAY DIFFRACTION24( CHAIN e AND RESID 338:366 )e338 - 366
30X-RAY DIFFRACTION25( CHAIN e AND RESID 367:403 )e367 - 403
31X-RAY DIFFRACTION26( CHAIN e AND RESID 404:489 )e404 - 489
32X-RAY DIFFRACTION27( CHAIN F AND RESID 2:99 )F2 - 99
33X-RAY DIFFRACTION28( CHAIN F AND RESID 100:236 )F100 - 236
34X-RAY DIFFRACTION29( CHAIN F AND RESID 237:288 )F237 - 288
35X-RAY DIFFRACTION30( CHAIN F AND RESID 289:324 ) OR ( CHAIN f AND RESID 330:489 )F289 - 324
36X-RAY DIFFRACTION30( CHAIN F AND RESID 289:324 ) OR ( CHAIN f AND RESID 330:489 )f330 - 489

+
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://pdbjlvh1.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