[English] 日本語
Yorodumi
- PDB-9b7i: Crystal structure of the H3 hemagglutinin COBRA J4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9b7i
TitleCrystal structure of the H3 hemagglutinin COBRA J4
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / hemagglutinin / antigen / receptor binding / membrane fusion
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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsDzimianski, J.V. / DuBois, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00052 United States
CitationJournal: To Be Published
Title: Assessing the structural boundaries of broadly reactive antibody interactions with diverse H3 influenza hemagglutinin proteins
Authors: Dzimianski, J.V. / Nagashima, K.A. / Cruz, J.M. / Sautto, G.A. / O'Rourke, S.M. / Serrao, V.B.H. / Ross, T.M. / Mousa, J.J. / DuBois, R.M.
History
DepositionMar 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)357,83449
Polymers340,76212
Non-polymers17,07237
Water00
1
A: Hemagglutinin HA1
B: Hemagglutinin HA1
C: Hemagglutinin HA1
a: Hemagglutinin HA2
b: Hemagglutinin HA2
c: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,80425
Polymers170,3816
Non-polymers8,42319
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42410 Å2
ΔGint-22 kcal/mol
Surface area59500 Å2
MethodPISA
2
D: Hemagglutinin HA1
E: Hemagglutinin HA1
F: Hemagglutinin HA1
d: Hemagglutinin HA2
e: Hemagglutinin HA2
f: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,03024
Polymers170,3816
Non-polymers8,64918
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42830 Å2
ΔGint-8 kcal/mol
Surface area60090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.744, 105.304, 109.682
Angle α, β, γ (deg.)71.610, 73.380, 87.070
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

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

#1: Protein
Hemagglutinin HA1


Mass: 36045.617 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A5J6A4B5
#2: Protein
Hemagglutinin HA2 / 2


Mass: 20748.119 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A5J6UNG5

-
Sugars , 6 types, 37 molecules

#3: 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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.: 5
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
#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.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-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 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-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
#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.: 18
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

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.3 M KNO3, 14% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.9→49.92 Å / Num. obs: 69687 / % possible obs: 92.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 56 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.077 / Rrim(I) all: 0.149 / Net I/σ(I): 7.5
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 1 / Num. unique obs: 3369 / CC1/2: 0.898 / Rpim(I) all: 0.232 / Rrim(I) all: 0.449 / % possible all: 89

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→49.92 Å / SU ML: 0.4781 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.9272
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2851 3507 5.04 %
Rwork0.2276 66011 -
obs0.2306 69518 92.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.92 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23203 0 1125 0 24328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003224807
X-RAY DIFFRACTIONf_angle_d0.568333574
X-RAY DIFFRACTIONf_chiral_restr0.04783896
X-RAY DIFFRACTIONf_plane_restr0.00474275
X-RAY DIFFRACTIONf_dihedral_angle_d17.60269435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.940.40461450.33112544X-RAY DIFFRACTION88.57
2.94-2.980.4011380.34792445X-RAY DIFFRACTION85.53
2.98-3.030.43231100.3182219X-RAY DIFFRACTION77.84
3.03-3.070.36731250.31752403X-RAY DIFFRACTION83.19
3.07-3.120.39851470.32282746X-RAY DIFFRACTION94.95
3.12-3.180.3971450.30312712X-RAY DIFFRACTION95.65
3.18-3.240.34231370.28152749X-RAY DIFFRACTION95.56
3.24-3.30.37271470.27742742X-RAY DIFFRACTION95.22
3.3-3.370.29651460.25162730X-RAY DIFFRACTION95.55
3.37-3.440.35871300.2542722X-RAY DIFFRACTION95.1
3.44-3.520.3451480.25592734X-RAY DIFFRACTION95.02
3.52-3.610.28541420.23792697X-RAY DIFFRACTION94.35
3.61-3.70.29281230.25842708X-RAY DIFFRACTION94.21
3.7-3.810.32941230.23872713X-RAY DIFFRACTION93.08
3.81-3.940.32231600.23282624X-RAY DIFFRACTION92.06
3.94-4.080.29491210.22222565X-RAY DIFFRACTION90.29
4.08-4.240.24861420.20612596X-RAY DIFFRACTION90.04
4.24-4.430.25621310.1872344X-RAY DIFFRACTION82.25
4.43-4.670.23421600.18092669X-RAY DIFFRACTION93.21
4.67-4.960.26121600.1822767X-RAY DIFFRACTION97.53
4.96-5.340.2321380.18112796X-RAY DIFFRACTION97.18
5.34-5.880.24921520.19442763X-RAY DIFFRACTION96.52
5.88-6.730.26421520.20232700X-RAY DIFFRACTION95
6.73-8.470.22711300.20652600X-RAY DIFFRACTION90.01
8.47-49.920.22211550.20192723X-RAY DIFFRACTION95.42
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)
11.6017801924-1.20366059426-1.092021034674.632475664451.46974031081.48803882670.2662391204570.0831989326677-0.385634889706-1.18996810416-0.4147546948740.638937922624-0.439502302994-0.2360400183910.1114429738390.4346928226430.0946758491647-0.0975218451850.566590984538-0.09612448244690.422435874206-41.6187.54226.521
21.77919040057-1.34981869108-0.5952360458330.8235240545420.4764011005810.1131287771120.5712424345940.1143784539830.474907562398-0.581771893149-0.376290957745-0.469807100489-0.5164734892440.067933094219-0.2143374111310.529083257396-0.09850260386070.1245360198270.4096900323910.0559327254270.559624272665-3.472-23.20517.395
31.19654139473-0.253752965929-0.3534423693351.5537546272-0.1146496013221.04151903207-0.2556870022780.149678021911-0.0380922278139-0.06453586607340.1477357071730.167351469946-0.1216440797320.006381144404150.1099795149480.464173569763-0.07373451460160.03451308250040.3985692531610.0939141420330.428918509004-1.916-35.57117.991
41.834098333450.00650048175331-0.4512370042322.631891916650.02813565716591.692596659950.0676087781643-0.157090455474-0.27865144715-0.0739187813499-0.118292854307-0.0963107644247-0.1761566274850.3874794992170.05333923752990.252612320765-0.09106732537020.002112831300690.470282638532-0.07049246864920.39995776232412.555-46.50919.259
51.34833659054-0.570550117849-0.9729244379672.702207911410.6326128578381.992056523460.1326639094940.379822465663-0.483330104443-0.306489696241-0.005124020840120.6107045101650.1620037460450.193765424646-0.1485411145890.2898044719580.0967751016198-0.09141704003070.480662461142-0.05608439895890.4711032125294.471-52.9415.125
63.207835042840.145842598144-0.8482124204151.01467134919-1.293699556191.69205987832-0.3087670496950.190178440462-0.3689715854650.2656965889410.2815094218490.865505651560.4036446789520.1345949863730.1461287810190.3260567412930.0397000814677-0.03527769127860.468167196041-0.1227212351470.7083573960891.529-55.14727.064
71.8174662139-0.4733368266110.2253638315492.743577843890.5046897796462.576831505530.197242868985-0.332011006268-0.196595055154-0.15645808372-0.1219274902210.099554403568-0.170196820995-0.375645366844-0.1041942157390.20472269628-0.06149904172110.01500109319710.4173152325870.06063102899010.3921682513680.407-48.68818.577
82.26065395993-1.13853630868-0.05030981183152.020484293970.2196714906711.39851022925-0.2672067624970.3600002774420.109889741376-0.0687887554950.242491024178-0.0860383344652-0.4025993445050.178396095932-0.002070697873860.350470324162-0.081936693776-0.02156440623560.3371324065630.01099721294460.2361163001351.635-36.41424.494
93.35608178447-0.863537568125-1.052466181461.40227611144-0.1046584065312.1282337843-0.1261056195350.04952611924010.704529996343-0.5675961386680.0090549421192-0.703609567983-0.3854409550020.02185071457130.09115102967290.440242310968-0.09834586609620.05558655777250.5039442436140.03515300336560.581360481198-15.164-14.92520.205
101.48328538873-1.30346880169-0.5024496577442.650214808830.2641321044440.2480033908780.249108932088-0.06872479899210.0349103102269-0.587868570023-0.1343437062340.203597369725-0.3464760965050.0599034009598-0.1166973777480.6849647656440.106162209077-0.05073751634260.5260581125480.02482187851980.202280124032-32.71-5.25524.415
113.09651363251-1.97318005706-0.9724991298062.859167341761.819349343461.998059904260.0518354447571-0.481621588540.6055163679580.4007210715790.388959845115-0.649252543086-0.207220297860.328665747987-0.4310009269830.563454344982-0.03471349897710.05989539277760.452872771806-0.03819886787840.341046972494-34.252.40555.801
121.42932351018-1.26120301267-0.2705499612281.3396067258-0.2963488169271.00014752866-0.112515794492-0.139922024867-0.3711306004550.6439113252360.09764748072020.330701756021-0.0228254799822-0.0253641917850.02288098125930.533508964825-0.0253314180440.07755618545290.3681981427590.07286097978930.48723876459-13.683-58.45446.999
132.874080214340.698418567182-0.2739185662492.470676891030.467283157792.59779703966-0.2657906858740.29211205404-0.779526263717-0.2904308270760.1071076878990.342000908533-0.217205444606-0.03683345560580.1447212072360.3934081724040.00118448924178-0.008946529266940.336024514488-0.07569497775040.589784769165-11.904-63.04134.244
141.18598774402-0.5054861155560.01611589981822.04656267610.2803242416530.122487775502-0.25003022108-0.195275135139-0.3564570785750.6892564872760.4790287785690.106876452290.0301903982951-0.234734737993-0.2213880930040.6944432828440.03335763529130.1375611037420.5282168055140.1383443850030.547171775262-20.537-46.99450.657
150.794352997489-0.4331795893571.110731304196.570146869070.1212130425751.4809807077-0.212850214591-0.1979215987770.2281759612620.430069191393-0.1048807663530.9870371974420.03363498336160.9635813274910.2637197137060.542191503928-0.02782447184540.1103569199380.523513881424-0.04579367783120.419385449984-24.791-27.32150.574
162.38517375339-1.33411187683-0.314272618382.672204308740.3278461564451.9887592158-0.189711554843-0.5350191867960.1218217874620.300697228740.287193988528-0.4647345062750.1283512965850.0298170315298-0.03932136698720.383033896144-0.08992198529470.02308525301560.402306655594-0.02037019812970.485283773071-28.331-10.48351.787
170.439292984772-0.796571004479-0.2333415625691.826690422050.599491509750.4964225997720.09791361248040.167124116308-0.513596664241-0.0299144709602-0.214477012640.6786441301350.105184079146-0.1420920868940.09191708330960.4170718116490.0137633560647-0.08085142242590.663554271509-0.1799273962551.04924645758-40.941-44.76719.959
182.894588901380.0818302597484-0.4730873103532.314712036810.3506224467841.843049079110.1854821990360.166973688708-0.707448856377-0.196367699026-0.5833374707290.780025625591-0.0402422889636-0.1486715665660.3973026271670.3641952568770.0200967493445-0.1394674384970.54537044919-0.2366425413110.806946061751-17.588-61.52410.735
191.12149327844-1.28940663183-0.4849642409091.749968773550.9219257646141.04703983240.1162930888730.00970381320257-0.79682741707-0.172849668804-0.1752646970350.831221325129-0.118178454969-0.108548887550.01862688608540.394140307190.0479509644749-0.1465285573660.506856441306-0.1232291424330.968227950008-39.773-41.95118.94
202.87307976403-2.472463636880.5477465617825.133965032621.067909947730.844299357179-0.429783096084-0.482478593644-0.6185166143040.2249917264590.160075434371.08884499477-0.0208619461136-0.3442126683220.1637669225570.358412776869-0.02859374875860.08510120393650.60366809872-0.169779318140.775440172843-51.498-21.17838.689
210.992705063488-1.391413427140.005866908131642.461064557080.8046509337190.663587236119-0.01930099504290.0094060587660.321660681619-0.1583962723690.170550981287-0.844322644117-0.1366217647620.200045786376-0.1085740810060.375403070464-0.1291501786120.04619787278350.4271713374240.0833597649340.650160755522-38.529.434-7.265
221.58064376613-0.528991521509-0.1642047390392.294850681620.04617722333832.70945994380.1001864225350.2114818223480.26566745125-0.0816133513959-0.0782366845207-0.01074410773-0.616672253917-0.1327254129370.03415473801250.363510698832-0.0487854304996-0.04567468501070.3160037894460.0688839186920.456460030465-60.49134.134-7.3
230.856251498236-1.26385532909-0.07291490068293.088657560520.332279883040.2162827160080.0478663615330.06650238619940.140044494583-0.1672058300280.00388099287618-0.4507186530550.03328166621940.0292638784654-0.04803895701210.351302562132-0.0677723837834-0.002217569887620.3925010650730.06546174394080.451724447433-46.02410.335-9.112
241.29423009212-1.04933957986-0.1756475322831.887109292630.7600670887691.117930379790.23604708040.44873748362-0.109243404667-0.506566683385-0.5426544469680.417660463603-0.301061685653-0.4020865067640.2729005697670.5144156967470.0210004773445-0.1211083262460.593280706167-0.08587730274930.446371636447-65.849-0.498-32.89
251.880253341-0.242068798623-0.8231818033621.282192464660.5051837897041.63098155940.1434679054390.201381168468-0.103667344851-0.214625750173-0.3185045420520.653658991553-0.218393944298-0.3683470080790.198313253330.4283226727550.166439868085-0.197260358170.686241111834-0.3368235808120.748561828029-83.03114.722-17.153
261.58277253749-1.029650475270.6038380599461.53005678015-1.362413440221.167663198570.2107999933450.806152041142-0.356388297159-0.673360614543-0.6597946507460.141362349583-0.005751418278380.4699229682510.3283598051070.6942773393460.154965278622-0.1675031157560.76730830458-0.1045674995290.403157552048-58.289-7.411-36.373
271.83022958952-0.2417135520310.07211986452082.964954492160.4231851678951.37209584860.01402065636970.2219707375780.14972906026-0.2617389242060.102852200526-0.357580247472-0.5274181480490.08030441767990.001431606221440.6006913998230.1469211679860.01567341243790.616785811550.2130418220570.229713521849-40.816-18.44-35.375
280.914029688815-1.3345174096-0.671028550072.902416696161.702352427051.32097743575-0.2455032593890.0376146292644-0.4261324097530.393086324758-0.2088662092360.7680406963570.240518389483-0.145855923510.3976496497920.478891050491-0.04954498182480.1144569316230.378337300108-0.002110256459720.547799349463-68.109-8.4635.677
292.54719995129-0.2103771413640.460703688830.8537794430881.352893370441.409336215480.2010155377250.585121400234-0.261031119740.062472196104-0.4962740220210.7131462249430.019125596667-0.375698995320.2417510284740.448051861022-0.000727583037368-0.03617908931040.405751273414-0.1076207131740.770824394721-80.63515.9335.235
301.21487650659-0.0988419467284-0.04342291075782.931094790110.2009249793221.846579611990.03111468855140.01740226852550.2352754003270.105180465001-0.284697197253-0.03170555701840.299284067464-0.1290118692820.216961980040.4326204795560.003712597401690.06461870299360.322400128959-0.08536073503160.531240998928-66.6516.58610
311.041106904-0.0817571500494-0.9908654597590.8349136987790.04120807435971.130506941090.00679728928949-0.116476067182-0.2842175274780.169402288245-0.09254501735150.6372105483590.1316578696660.02946420732770.08971031395210.366030677529-0.04008546308860.05097590396490.3157754278330.01488890188620.593142262692-58.808-27.607-6.845
321.49651229225-0.4115531305580.3166947421472.218037517830.5605041599840.3443348356050.08522371987270.2376513261310.209020262034-0.141405084231-0.129509508393-0.0645200602521-0.3392038841090.1208515300380.02074764972910.583539235638-0.01023861317360.04502446358970.4862682487820.06025365147750.293364667175-38.4714.20532.78
330.00244595243391-0.002460796731060.04686076397290.00476826582419-0.0128678797530.08869067278790.170078741099-0.6029265557251.55866676214-0.0462554546807-0.15184227569-0.0105498980825-0.286833205628-0.61170370142-0.05885559428520.3552827375230.1070381396690.04154333360480.649345001637-0.09375121735790.99360274202-15.791-17.09630.915
341.22295865659-0.511804011632-0.08748306890061.681562551320.4931861183330.4325584682760.2203871468540.151031592840.0536027454201-0.230893783087-0.3674116483690.125933762859-0.255749644276-0.222777419320.09502777909030.492521960680.030212240008-0.04372733538840.4226102019080.003986200163630.23518837805-40.1074.8936.196
351.77651606329-0.2633580646870.3813432687042.459235112660.3545585353911.61972074883-0.205371681412-0.4867472104780.001858282818170.4416245232250.222407289307-0.0507692674233-0.123153863943-0.1682920684680.04383025240260.6015442578860.009288721127510.1200823004850.520749243651-0.008060974476120.366739376467-42.6571.72959.864
364.851439659170.739694621177-1.806187961650.917498315088-0.6570262785312.880558607410.560291949591-0.360025664250.154226910890.21612324127-0.2155656166130.0691141312965-0.0585012796906-0.00339845166049-0.327538895480.574517502665-0.07200787594890.05590335081110.34627065990.00888413361020.584687459194-21.83-36.02542.589
371.48382476149-0.547247178795-0.1189640799452.338844360120.4632069700110.472864587534-0.119680250441-0.5021058298840.04981181790060.2955367708870.1399867438340.333605757593-0.1971983063250.0717963556906-0.0507950039360.500740223597-0.04594631258180.05382251215580.422131223070.00733076705970.275939331044-45.0531.86252.143
381.85663528731-0.3035698137990.5156332245851.68716968287-0.4321171428212.009560133240.06353206012950.190143313909-0.1503566065860.221402778132-0.01702373810530.9396018114790.392857875816-0.000832083074998-0.0729185907140.5533287548180.08394716529740.1048658570050.612468977925-0.2353731477051.09160358968-63.057-2.84938.136
393.16041951008-0.7401406379671.063634601571.40713642871-0.3734410582863.02157598855-0.228871890608-0.589669424426-0.752134735642-0.08958696918580.3397121131260.423134276995-0.230059547793-0.500768821297-0.2505548988140.42576887985-0.0194562623119-0.004905529393910.570181024628-0.0936149865411.06984047258-35.563-37.6326.37
401.50345321412-1.12385557106-0.3502401970343.400865216840.6704208053550.4232141251770.18376987770.2082421011660.05298361516150.0659953616231-0.5197056517920.627643508347-0.0950975167293-0.2629141751390.3062240356360.385620370420.0651045123810.01901584949560.517579647921-0.02622776139230.302619166097-55.456-0.03740.289
411.75917762598-0.397211131222-0.5127768227351.64740172933-0.3429987343160.8464440864670.145159315535-0.2367150460580.280172025288-0.166786849350.225484068278-1.026692126060.2706382994870.507258280201-0.3691758191750.6331352962180.1794322745740.03415319156580.756453765317-0.1237878124151.22485496183-15.426-32.749-19.79
420.6149588990210.2277125716610.06752918432020.969066584958-1.278954289391.94993103242-0.6595712524780.1694349662440.1655814121460.160991271525-0.170609315794-0.529650502429-0.3450578452660.244980187750.7653129225880.4271399400510.0611668119305-0.1745751525770.85866403362-0.1929520387240.937680908666-41.0210.875-15.465
433.774771684351.99233750493-2.209702348891.617003157220.4897040013796.50510666717-0.169047948177-0.2215781703440.3277108439510.00897733311672-0.5611663724140.0530226214633-0.3910763259760.678260492260.6630575372880.4527688656020.0200708897532-0.05120679741720.3386759528330.1387660887410.692971952018-52.2053.7850.021
441.41308771949-0.248110573361-0.07610529159171.02732860374-0.04993842957271.17115617806-0.15830990360.170093749196-0.8812855741590.2868512666340.08067393476050.02841835119570.375754205910.4194964733960.02662001131030.3598756420540.0868935931239-0.04467784394990.492023550837-0.01900990017810.665456450703-28.254-30.35-19.395
450.00102287084520.2211807309840.02027889208413.242555935750.8556234372170.5738124804810.4359183563620.617831042483-0.609118640814-1.10741868275-0.370382014792-0.572479277085-0.472262442133-0.40144211962-0.03401689773380.969162290550.3969978560710.1252823627561.27277440083-0.3727416338211.59159503315-6.256-49.935-33.547
461.92444088620.512191711760.02720278036151.472481757840.002848858807221.557798719530.21724272850.835281772141-0.428833146541-0.260041069937-0.157979313905-0.277817742490.0894433059460.02898728679140.01688100220290.6837518858610.140029219830.02153477364290.824831688267-0.1794810090490.678469067236-33.974-38.675-43.34
470.00618127906337-0.004183307616343.03548961374E-5-0.01405104973810.0227108036007-0.007383521710570.01165722130740.478191444154-1.0739145993-0.5141674344410.0769347340139-0.431680133668-0.1678318636120.1871982699560.0121220994840.617706918130.04177075158960.006678031495720.659944171253-0.2172303883220.855991937615-58.028-17.818-27.97
481.17986068956-1.40793169583-0.5966306704641.930731877071.238172394051.476629229530.4465987991880.481141451221-0.2138207429-0.664268796498-0.488245036308-0.0396619448104-0.0189654667240.06008968791150.06098153613360.4767979054010.08042810915840.02550753997380.622319573541-0.0887991398450.522322937581-36.143-33.723-33.2
491.35459018678-0.341342664065-0.2986193641211.57427302064-0.1312867684261.987820342340.1158587699470.0483284863233-0.391604166983-0.272349515675-0.178312610127-0.002910905988280.382591804134-0.1133753529220.0936647962450.7333750853220.09525985125250.01185986403360.473700619059-0.06053271004960.613618381209-39.283-51.028-15.985
501.368068115920.3306989161960.9804306067781.522707395280.7526694235210.8973523724780.543813710050.196746740703-0.560334035096-0.1122150948830.2513593636920.07119689737560.3793738400840.382467552551-0.6756556281280.766595411266-0.05824834833550.1394933468680.757187839137-0.03448742894510.406951600004-52.628-18.13-1.12
510.730442238194-0.4929329678870.387129183942.783996388310.4540332107080.8432529068050.2017992344490.210569664183-0.571377492203-0.214700944316-0.1676527215950.2211302436640.3312529096680.114273611255-0.004366522502170.4773566344750.03064000494290.03925904917770.417154714392-0.04223051301430.439067442277-38.119-41.791-19.32
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 8:41 )A8 - 41
2X-RAY DIFFRACTION2( CHAIN A AND RESID 42:89 )A42 - 89
3X-RAY DIFFRACTION3( CHAIN A AND RESID 90:122 )A90 - 122
4X-RAY DIFFRACTION4( CHAIN A AND RESID 123:175 )A123 - 175
5X-RAY DIFFRACTION5( CHAIN A AND RESID 176:195 )A176 - 195
6X-RAY DIFFRACTION6( CHAIN A AND RESID 196:214 )A196 - 214
7X-RAY DIFFRACTION7( CHAIN A AND RESID 215:247 )A215 - 247
8X-RAY DIFFRACTION8( CHAIN A AND RESID 248:269 )A248 - 269
9X-RAY DIFFRACTION9( CHAIN A AND RESID 270:303 )A270 - 303
10X-RAY DIFFRACTION10( CHAIN A AND RESID 304:325 )A304 - 325
11X-RAY DIFFRACTION11( CHAIN B AND RESID 8:41 )B8 - 41
12X-RAY DIFFRACTION12( CHAIN B AND RESID 42:195 )B42 - 195
13X-RAY DIFFRACTION13( CHAIN B AND RESID 196:247 )B196 - 247
14X-RAY DIFFRACTION14( CHAIN B AND RESID 248:288 )B248 - 288
15X-RAY DIFFRACTION15( CHAIN B AND RESID 289:303 )B289 - 303
16X-RAY DIFFRACTION16( CHAIN B AND RESID 304:326 )B304 - 326
17X-RAY DIFFRACTION17( CHAIN C AND RESID 8:153 )C8 - 153
18X-RAY DIFFRACTION18( CHAIN C AND RESID 154:247 )C154 - 247
19X-RAY DIFFRACTION19( CHAIN C AND RESID 248:304 )C248 - 304
20X-RAY DIFFRACTION20( CHAIN C AND RESID 305:325 )C305 - 325
21X-RAY DIFFRACTION21( CHAIN D AND RESID 9:146 )D9 - 146
22X-RAY DIFFRACTION22( CHAIN D AND RESID 147:201 )D147 - 201
23X-RAY DIFFRACTION23( CHAIN D AND RESID 202:325 )D202 - 325
24X-RAY DIFFRACTION24( CHAIN E AND RESID 10:146 )E10 - 146
25X-RAY DIFFRACTION25( CHAIN E AND RESID 147:269 )E147 - 269
26X-RAY DIFFRACTION26( CHAIN E AND RESID 270:303 )E270 - 303
27X-RAY DIFFRACTION27( CHAIN E AND RESID 304:325 )E304 - 325
28X-RAY DIFFRACTION28( CHAIN F AND RESID 8:184 )F8 - 184
29X-RAY DIFFRACTION29( CHAIN F AND RESID 185:228 )F185 - 228
30X-RAY DIFFRACTION30( CHAIN F AND RESID 229:269 )F229 - 269
31X-RAY DIFFRACTION31( CHAIN F AND RESID 270:325 )F270 - 325
32X-RAY DIFFRACTION32( CHAIN a AND RESID 330:384 )a330 - 384
33X-RAY DIFFRACTION33( CHAIN a AND RESID 385:394 )a385 - 394
34X-RAY DIFFRACTION34( CHAIN a AND RESID 395:501 )a395 - 501
35X-RAY DIFFRACTION35( CHAIN b AND RESID 330:385 )b330 - 385
36X-RAY DIFFRACTION36( CHAIN b AND RESID 386:404 )b386 - 404
37X-RAY DIFFRACTION37( CHAIN b AND RESID 405:500 )b405 - 500
38X-RAY DIFFRACTION38( CHAIN c AND RESID 330:384 )c330 - 384
39X-RAY DIFFRACTION39( CHAIN c AND RESID 385:404 )c385 - 404
40X-RAY DIFFRACTION40( CHAIN c AND RESID 405:501 )c405 - 501
41X-RAY DIFFRACTION41( CHAIN d AND RESID 330:384 )d330 - 384
42X-RAY DIFFRACTION42( CHAIN d AND RESID 385:396 )d385 - 396
43X-RAY DIFFRACTION43( CHAIN d AND RESID 397:404 )d397 - 404
44X-RAY DIFFRACTION44( CHAIN d AND RESID 405:476 )d405 - 476
45X-RAY DIFFRACTION45( CHAIN d AND RESID 477:501 )d477 - 501
46X-RAY DIFFRACTION46( CHAIN e AND RESID 330:382 )e330 - 382
47X-RAY DIFFRACTION47( CHAIN e AND RESID 383:392 )e383 - 392
48X-RAY DIFFRACTION48( CHAIN e AND RESID 393:500 )e393 - 500
49X-RAY DIFFRACTION49( CHAIN f AND RESID 330:384 )f330 - 384
50X-RAY DIFFRACTION50( CHAIN f AND RESID 385:394 )f385 - 394
51X-RAY DIFFRACTION51( CHAIN f AND RESID 395:501 )f395 - 501

+
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