[English] 日本語
Yorodumi
- PDB-6osr: Crystal structure of Influenza hemagglutinin from strain A/Melbou... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6osr
TitleCrystal structure of Influenza hemagglutinin from strain A/Melbourne/1/1946(H1N1)
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / Inflenza hemagglutinin / 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
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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 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
DepositionMay 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
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_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.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 2.1May 24, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 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
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)367,97139
Polymers362,8546
Non-polymers5,11833
Water11,602644
1
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,69820
Polymers181,4273
Non-polymers3,27117
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14730 Å2
ΔGint-22 kcal/mol
Surface area59870 Å2
MethodPISA
2
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,27419
Polymers181,4273
Non-polymers1,84716
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14700 Å2
ΔGint-36 kcal/mol
Surface area58250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.100, 113.970, 246.380
Angle α, β, γ (deg.)90.000, 91.440, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 5 and (name N or name...
21(chain B and ((resid 5 and (name N or name...
31(chain C and ((resid 5 and (name N or name...
41(chain D and ((resid 5 and (name N or name...
51(chain E and (resid 5 through 22 or (resid 23...
61(chain F and ((resid 5 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 5 and (name N or name...A5
121(chain A and ((resid 5 and (name N or name...A4 - 504
131(chain A and ((resid 5 and (name N or name...A4 - 504
141(chain A and ((resid 5 and (name N or name...A4 - 504
151(chain A and ((resid 5 and (name N or name...A4 - 504
211(chain B and ((resid 5 and (name N or name...B5
221(chain B and ((resid 5 and (name N or name...B2 - 501
231(chain B and ((resid 5 and (name N or name...B2 - 501
241(chain B and ((resid 5 and (name N or name...B2 - 501
251(chain B and ((resid 5 and (name N or name...B2 - 501
311(chain C and ((resid 5 and (name N or name...C5
321(chain C and ((resid 5 and (name N or name...C4 - 503
331(chain C and ((resid 5 and (name N or name...C4 - 503
341(chain C and ((resid 5 and (name N or name...C4 - 503
351(chain C and ((resid 5 and (name N or name...C4 - 503
411(chain D and ((resid 5 and (name N or name...D5
421(chain D and ((resid 5 and (name N or name...D4 - 501
431(chain D and ((resid 5 and (name N or name...D4 - 501
441(chain D and ((resid 5 and (name N or name...D4 - 501
451(chain D and ((resid 5 and (name N or name...D4 - 501
511(chain E and (resid 5 through 22 or (resid 23...E5 - 22
521(chain E and (resid 5 through 22 or (resid 23...E23 - 24
531(chain E and (resid 5 through 22 or (resid 23...E5 - 502
541(chain E and (resid 5 through 22 or (resid 23...E5 - 502
551(chain E and (resid 5 through 22 or (resid 23...E5 - 502
561(chain E and (resid 5 through 22 or (resid 23...E5 - 502
611(chain F and ((resid 5 and (name N or name...F5
621(chain F and ((resid 5 and (name N or name...F4 - 503
631(chain F and ((resid 5 and (name N or name...F4 - 503
641(chain F and ((resid 5 and (name N or name...F4 - 503
651(chain F and ((resid 5 and (name N or name...F4 - 503

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Hemagglutinin /


Mass: 60475.586 Da / Num. of mol.: 6 / Fragment: UNP residues 18-509
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Melbourne/1/1946(H1N1))
Strain: A/Melbourne/1/1946(H1N1) / Gene: HA / Plasmid: InvbX.18715.a / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C7S1Y2

-
Sugars , 2 types, 17 molecules

#2: 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
#3: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 16
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

-
Non-polymers , 4 types, 660 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: K
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H2O

-
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: 8.5
Details: 0.1 uL 10.1 mg/mL SEC-purified InvbX.18715.a.KN11.PD38349 in 25 mM Tris, pH 8.5, 150 mM sodium chloride + 0.1 uL mother liquor (0.2 M potassium citrate, 20% PEG3350, 3% 1,5-pentanediol), ...Details: 0.1 uL 10.1 mg/mL SEC-purified InvbX.18715.a.KN11.PD38349 in 25 mM Tris, pH 8.5, 150 mM sodium chloride + 0.1 uL mother liquor (0.2 M potassium citrate, 20% PEG3350, 3% 1,5-pentanediol), cryoprotection: mother liquor + 20% ethylene glycol, Crystal ID 308017b5, data set yxj7-1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 21, 2019
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.55→48.736 Å / Num. obs: 131565 / % possible obs: 99.8 % / Redundancy: 5.256 % / Biso Wilson estimate: 46.927 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.168 / Rrim(I) all: 0.186 / Χ2: 0.974 / Net I/σ(I): 7.78 / Num. measured all: 691488 / Scaling rejects: 35
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
2.55-2.625.2841.0891.5251334974097150.5481.2199.7
2.62-2.695.3020.9461.7649968944194240.6351.0599.8
2.69-2.775.3050.7972.1448541916891500.7070.88499.8
2.77-2.855.3130.6532.647447895089300.7970.72599.8
2.85-2.945.3280.523.2446340870686980.8520.57799.9
2.94-3.055.3420.4353.8944764838683800.8880.48299.9
3.05-3.165.3320.3334.8942990807080620.9380.36999.9
3.16-3.295.3440.2666.0841556778377760.9590.29699.9
3.29-3.445.2960.217.4639470745674530.9770.233100
3.44-3.615.2790.1689.2137583712471200.9790.18799.9
3.61-3.85.2470.13610.7535904684968430.9870.15199.9
3.8-4.035.2080.11512.1433568644864450.990.128100
4.03-4.315.1730.09614.0131449608160790.9920.107100
4.31-4.665.1510.08515.628905562556110.9920.09599.8
4.66-5.15.1450.08315.7426683519551860.9940.09299.8
5.1-5.75.1590.08315.1324419474047330.9930.09399.9
5.7-6.585.1470.08614.8221397415941570.9920.096100
6.58-8.065.1530.07316.5618304355935520.9930.08299.8
8.06-11.45.0330.05519.2813781274427380.9960.06299.8
11.4-48.7364.6830.05519.527085156115130.9970.06396.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIXdev_3409refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MYA

6mya


Resolution: 2.55→48.736 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 1954 1.49 %
Rwork0.1912 129570 -
obs0.1921 131524 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 210.05 Å2 / Biso mean: 55.7642 Å2 / Biso min: 6.4 Å2
Refinement stepCycle: final / Resolution: 2.55→48.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22122 0 323 646 23091
Biso mean--89.94 42.21 -
Num. residues----2870
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10647X-RAY DIFFRACTION10.049TORSIONAL
12B10647X-RAY DIFFRACTION10.049TORSIONAL
13C10647X-RAY DIFFRACTION10.049TORSIONAL
14D10647X-RAY DIFFRACTION10.049TORSIONAL
15E10647X-RAY DIFFRACTION10.049TORSIONAL
16F10647X-RAY DIFFRACTION10.049TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5501-2.61380.311340.26592709404
2.6138-2.68450.3081410.259291079248
2.6845-2.76350.33371380.252292259363
2.7635-2.85270.31531180.241792349352
2.8527-2.95460.33221410.235792189359
2.9546-3.07290.31311710.233892329403
3.0729-3.21270.28161300.222892209350
3.2127-3.38210.2711240.195692499373
3.3821-3.59390.22741350.181792489383
3.5939-3.87130.23741460.171993169462
3.8713-4.26070.1771230.150792419364
4.2607-4.87670.18731580.140592859443
4.8767-6.14220.19521300.175593239453
6.1422-48.74540.25481650.199494029567
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)
11.3166-0.7231-1.40760.70950.82723.8745-0.1171-0.4649-0.12040.42830.18880.01930.27030.1746-0.01910.47560.0357-0.05410.33560.060.349421.5238-15.193653.8828
21.4401-0.0269-0.78531.89670.06342.97780.05110.1525-0.0929-0.08470.0099-0.0286-0.03990.0036-0.06350.22480.0068-0.09170.146-0.01350.297226.4793-15.39320.219
31.1536-0.1809-0.51890.60540.1111.4449-0.1805-0.7018-0.25030.39880.13590.19870.43940.13080.0680.76760.09690.03640.76920.13590.35427.0272-9.298480.205
41.27130.352-1.59150.7321-1.23057.92010.0785-0.06060.10550.2436-0.00340.2496-0.1349-0.7969-0.06660.3342-0.00250.00950.3256-0.01150.4437-16.359-1.451.8993
53.01370.3515-1.21681.2642-0.63193.2725-0.15130.5075-0.1299-0.1740.17160.0810.0906-0.237-0.02250.2450.0022-0.11570.3035-0.02710.3697-0.88714.830915.9745
60.8806-0.0245-0.74150.68520.09193.3001-0.0245-0.4291-0.06610.369-0.02570.2053-0.1207-0.4570.03540.50230.04560.04120.62620.03210.3504-13.35151.191574.0388
71.39930.3946-1.50840.4992-0.92432.24040.2963-0.31240.30860.4197-0.0450.1331-0.5082-0.0401-0.25560.4915-0.04880.02430.3672-0.12710.379417.387722.948152.5668
81.2963-0.1166-0.80131.17410.34533.10810.08960.01670.1378-0.0161-0.06350.0307-0.097-0.1109-0.02750.2467-0.0208-0.06580.1625-0.02790.335629.807618.900224.7881
91.04830.2044-0.73660.35120.07793.44040.1997-0.62540.21670.50940.01330.082-0.27790.2512-0.1910.74090.00860.07640.6442-0.10650.35865.112814.141975.828
100.63520.14520.60580.11670.11070.57050.1546-0.97150.3750.99440.16520.2235-0.91370.3983-0.13951.631-0.11080.26921.7258-0.22910.5311-1.272115.3315113.148
110.8568-0.0721-0.20290.5218-0.14043.5498-0.0543-0.23910.04240.03290.05810.1610.2992-0.401-0.01510.2528-0.0384-0.03090.2996-0.00770.357422.2124-51.143247.0369
123.12050.4972-3.61053.1115-1.35815.08210.04250.371-0.1677-0.0590.04190.18140.0056-0.474-0.08750.2934-0.0154-0.16560.2288-0.02650.304630.3644-46.7819.29
132.204-1.0088-0.63094.16260.9782.6618-0.11390.13230.0057-0.21620.1805-0.19240.04510.0173-0.08910.2461-0.0327-0.04510.15290.00370.238140.3717-47.753416.5799
145.54234.1591-3.61194.4696-4.17475.2556-0.104-0.59520.1132-0.0221-0.1316-0.15720.0115-0.02430.2060.21640.0832-0.01530.2551-0.08460.32322.126-45.023441.2662
150.76040.0639-0.98210.6802-0.89656.55250.0634-0.28560.11530.4893-0.13740.16240.0455-0.29530.03770.4472-0.06650.03710.6507-0.050.290821.2994-54.360767.8714
161.5276-0.9186-0.18423.2121.9091.2385-0.0319-0.1562-0.17130.95030.20350.614-0.6156-0.355-0.15431.0911-0.11590.26091.5214-0.06630.54377.2001-51.121995.8336
171.614-0.4669-2.14360.59740.83015.39340.1127-0.49940.21440.35550.12930.0543-0.215-0.3242-0.22660.4950.03630.07010.6568-0.05510.307728.1412-52.24372.5014
180.647-0.7011-0.49190.7580.52830.36970.0764-0.92880.47360.49320.173-0.02170.5514-0.362-0.19341.39360.15070.52122.0172-0.24230.61689.7708-46.167108.7773
190.48910.1217-1.66040.1854-0.21465.54920.3962-0.70340.49970.4383-0.06830.0288-0.42010.1023-0.27830.7449-0.04680.00120.7529-0.23990.459144.3468-35.741580.9163
202.0643-0.12540.02791.274-0.10251.8053-0.01080.12820.1389-0.07190.0048-0.0722-0.20290.07250.0020.2241-0.0662-0.03180.2754-0.05040.321966.5192-41.522931.2915
210.80210.1377-0.15250.4379-0.34722.65590.1755-0.70380.21650.5512-0.0227-0.067-0.32620.0178-0.12190.7717-0.0201-0.00980.8508-0.1710.323742.8247-43.613484.7473
220.6908-0.2739-0.2920.60390.96342.6274-0.0632-0.4303-0.21390.51940.2028-0.09320.82220.1587-0.09530.66890.1054-0.09030.48390.07490.406649.5109-75.710865.2108
231.7440.6364-0.12112.04840.15872.399-0.11460.1426-0.2032-0.10740.205-0.37050.00350.2821-0.080.2238-0.0021-0.05370.2125-0.07890.356754.9373-73.767625.2398
240.83990.0364-1.16880.28820.70744.6181-0.1948-0.6345-0.26340.61820.17190.03110.47570.06580.05660.81330.0816-0.04360.76070.0980.366643.4211-72.29880.05
252.9483.2204-3.90653.4611-4.36018.36530.21020.32120.29460.61910.48410.23440.1545-1.4315-0.63280.67950.0758-0.04470.5650.11660.387737.9046-67.625768.424
260.98950.2083-1.5080.8783-0.39314.98130.1659-0.6013-0.02150.79780.0014-0.05090.0778-0.0447-0.13820.8455-0.0747-0.01660.75430.04530.21238.3721-59.74981.0011
270.13370.01110.10830.1609-0.14060.2217-0.4948-0.8743-0.43510.9610.25010.42710.5485-0.34190.13521.9880.10210.45251.70360.40540.740824.0401-71.012113.987
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 117 )A4 - 117
2X-RAY DIFFRACTION2chain 'A' and (resid 118 through 269 )A118 - 269
3X-RAY DIFFRACTION3chain 'A' and (resid 270 through 492 )A270 - 492
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 83 )B2 - 83
5X-RAY DIFFRACTION5chain 'B' and (resid 84 through 280 )B84 - 280
6X-RAY DIFFRACTION6chain 'B' and (resid 281 through 486 )B281 - 486
7X-RAY DIFFRACTION7chain 'C' and (resid 4 through 117 )C4 - 117
8X-RAY DIFFRACTION8chain 'C' and (resid 118 through 284 )C118 - 284
9X-RAY DIFFRACTION9chain 'C' and (resid 285 through 458 )C285 - 458
10X-RAY DIFFRACTION10chain 'C' and (resid 459 through 492 )C459 - 492
11X-RAY DIFFRACTION11chain 'D' and (resid 4 through 117 )D4 - 117
12X-RAY DIFFRACTION12chain 'D' and (resid 118 through 162 )D118 - 162
13X-RAY DIFFRACTION13chain 'D' and (resid 163 through 254 )D163 - 254
14X-RAY DIFFRACTION14chain 'D' and (resid 255 through 284 )D255 - 284
15X-RAY DIFFRACTION15chain 'D' and (resid 285 through 337 )D285 - 337
16X-RAY DIFFRACTION16chain 'D' and (resid 338 through 366 )D338 - 366
17X-RAY DIFFRACTION17chain 'D' and (resid 367 through 461 )D367 - 461
18X-RAY DIFFRACTION18chain 'D' and (resid 462 through 491 )D462 - 491
19X-RAY DIFFRACTION19chain 'E' and (resid 5 through 48 )E5 - 48
20X-RAY DIFFRACTION20chain 'E' and (resid 49 through 269 )E49 - 269
21X-RAY DIFFRACTION21chain 'E' and (resid 270 through 492 )E270 - 492
22X-RAY DIFFRACTION22chain 'F' and (resid 4 through 83 )F4 - 83
23X-RAY DIFFRACTION23chain 'F' and (resid 84 through 269 )F84 - 269
24X-RAY DIFFRACTION24chain 'F' and (resid 270 through 366 )F270 - 366
25X-RAY DIFFRACTION25chain 'F' and (resid 367 through 403 )F367 - 403
26X-RAY DIFFRACTION26chain 'F' and (resid 404 through 461 )F404 - 461
27X-RAY DIFFRACTION27chain 'F' and (resid 462 through 492 )F462 - 492

+
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