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- PDB-9hls: Structure of A16/G9 (vaccinia virus) in complex with VHH D07, VHH... -

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Basic information

Entry
Database: PDB / ID: 9hls
TitleStructure of A16/G9 (vaccinia virus) in complex with VHH D07, VHH B01 and VHH C05
Components
  • Entry-fusion complex protein OPG094
  • VHH B01
  • VHH C05
  • VHH D07
  • Virion membrane protein OPG143
KeywordsVIRAL PROTEIN / poxvirus / viral fusion / vaccinia virus / mpox virus
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / DNA-templated transcription termination / helicase activity / hydrolase activity / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / virion membrane / DNA binding / ATP binding / membrane
Similarity search - Function
Pox virus entry-fusion-complex G9/A16 / Pox virus entry-fusion-complex G9/A16
Similarity search - Domain/homology
: / PHOSPHATE ION / Entry-fusion complex protein OPG094 / Virion membrane protein OPG143
Similarity search - Component
Biological speciesVaccinia virus Western Reserve
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsVernuccio, R. / Meola, A. / Guardado-Calvo, P.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-22-CE11-0003 France
CitationJournal: Cell / Year: 2025
Title: Structural basis of poxvirus fusion regulation and anti-A16/G9 antibody-mediated neutralization and protection.
Authors: Annalisa Meola / Riccardo Vernuccio / Leandro Battini / Guillermo Albericio / Pilar Delgado / Rebecca Bamford / Laura Pokorny / Manon Broutin / Alejandro Martínez León / Sébastien Gallien ...Authors: Annalisa Meola / Riccardo Vernuccio / Leandro Battini / Guillermo Albericio / Pilar Delgado / Rebecca Bamford / Laura Pokorny / Manon Broutin / Alejandro Martínez León / Sébastien Gallien / María Gil / María A Noriega / Florence Guivel-Benhassine / Françoise Porrot / Jeanne Postal / Julian Buchrieser / Mathieu Hubert / Ahmed Haouz / Pierre Lafaye / Mariano Esteban / Jochen S Hub / Matthieu Mahévas / Pascal Chappert / Jason Mercer / Juan Garcia-Arriaza / Olivier Schwartz / Pablo Guardado-Calvo /
Abstract: Monkeypox virus (MPXV) is a poxvirus endemic to Central and West Africa with high epidemic potential. Poxviruses enter host cells via a conserved entry-fusion complex (EFC), which mediates viral ...Monkeypox virus (MPXV) is a poxvirus endemic to Central and West Africa with high epidemic potential. Poxviruses enter host cells via a conserved entry-fusion complex (EFC), which mediates viral fusion to the cell membrane. The EFC is a promising therapeutic target, but the absence of structural data has limited the development of fusion-inhibiting treatments. Here, we investigated A16/G9, a subcomplex of the EFC that controls fusion timing. Using cryo-electron microscopy, we showed how A16/G9 interacts with A56/K2, a viral fusion suppressor that prevents superinfection. Immunization with A16/G9 elicited a protective immune response in mice. Using X-ray crystallography, we characterized two neutralizing antibodies and engineered a chimeric antibody that cross-neutralizes several poxviruses more efficiently than 7D11, the most potent antibody targeting the EFC described to date. These findings highlight the potential of A16/G9 as a candidate for subunit vaccines and identify regions of the EFC as targets for antiviral development.
History
DepositionDec 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Virion membrane protein OPG143
B: Entry-fusion complex protein OPG094
C: VHH D07
D: VHH B01
J: VHH C05
F: Virion membrane protein OPG143
G: Entry-fusion complex protein OPG094
H: VHH D07
I: VHH B01
E: VHH C05
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,53717
Polymers259,09610
Non-polymers4417
Water1086
1
A: Virion membrane protein OPG143
B: Entry-fusion complex protein OPG094
C: VHH D07
D: VHH B01
E: VHH C05
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,6827
Polymers129,5485
Non-polymers1342
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
J: VHH C05
F: Virion membrane protein OPG143
G: Entry-fusion complex protein OPG094
H: VHH D07
I: VHH B01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,85510
Polymers129,5485
Non-polymers3075
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.435, 194.282, 94.866
Angle α, β, γ (deg.)90.000, 91.263, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "F"
d_1ens_2chain "B"
d_2ens_2chain "G"
d_1ens_3(chain "C" and (resid 3 through 40 or resid 45 through 119))
d_2ens_3chain "H"
d_1ens_4chain "D"
d_2ens_4chain "I"
d_1ens_5chain "E"
d_2ens_5(chain "J" and resid 3 through 122)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1VALVALCYSCYSAA5 - 29124 - 310
d_21ens_1VALVALCYSCYSFF5 - 29124 - 310
d_11ens_2VALVALASNASNBB7 - 26824 - 285
d_21ens_2VALVALASNASNGG7 - 26824 - 285
d_11ens_3GLUGLUARGARGCC3 - 403 - 40
d_12ens_3LYSLYSSERSERCC45 - 11945 - 119
d_21ens_3GLUGLUSERSERHH3 - 1193 - 119
d_11ens_4VALVALVALVALDD4 - 1204 - 120
d_21ens_4VALVALVALVALII4 - 1204 - 120
d_11ens_5ASPASPSERSEREJ3 - 1223 - 122
d_21ens_5ASPASPSERSERJE3 - 1223 - 122

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixVector
1given(0.999527080807, 9.2062050342E-5, 0.0307507114915), (-0.000660172751443, -0.99970080415, 0.0244513057542), (0.0307437620436, -0.0244600430442, -0.999227965676)-0.300028873193, 27.3871913077, -1.97578892024
2given(0.999138236426, 5.62681381275E-5, 0.0415064012615), (-0.000330191182701, -0.999956663062, 0.00930392237991), (0.0415051260155, -0.00930960964623, -0.999094918255)-0.209564444947, 27.6990750987, -2.56662197876
3given(0.99757359318, 0.0194307571296, 0.0668533609299), (0.0175357487378, -0.999430883282, 0.0288167843271), (0.067375245502, -0.0275745393455, -0.997346590245)-0.52953252305, 26.8045351211, -3.61381979624
4given(0.98912359383, 0.0299559623672, 0.14400401539), (0.0270451780916, -0.999389249701, 0.0221288482542), (0.14457895584, -0.0179935516704, -0.989329650635)-1.80366595868, 26.7842788013, -5.14937444416
5given(0.998358396782, -0.0197672799237, 0.0537565458192), (-0.0198298880813, -0.999803169015, 0.000631479613251), (0.053733482231, -0.00169642926152, -0.998553871864)-0.158625444702, 28.8577446395, -3.06632479026

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Components

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Protein , 2 types, 4 molecules AFBG

#1: Protein Virion membrane protein OPG143


Mass: 40941.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus Western Reserve / Gene: OPG143, VACWR136, A16L / Cell line (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P16710
#2: Protein Entry-fusion complex protein OPG094 / EFC protein OPG094 / Myristoylated protein G9 / Protein F1


Mass: 37432.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus Western Reserve / Gene: OPG094, VACWR087, G9R / Cell line (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P07611

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Antibody , 3 types, 6 molecules CHDIJE

#3: Antibody VHH D07


Mass: 16965.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli BL21(DE3) (bacteria)
#4: Antibody VHH B01


Mass: 17044.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Antibody VHH C05


Mass: 17163.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 3 types, 13 molecules

#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 20% w/v PEG 3350, 0.2 M KH2PO4 (cryoprotected with 33% Ethylene glycol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 3.2→39.72 Å / Num. obs: 44399 / % possible obs: 99 % / Redundancy: 5.9 % / Biso Wilson estimate: 66.43 Å2 / CC1/2: 0.971 / Net I/σ(I): 4.2
Reflection shellResolution: 3.2→3.32 Å / Num. unique obs: 4713 / CC1/2: 0.563

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→39.72 Å / SU ML: 0.4898 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.965
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2923 2117 4.78 %
Rwork0.2367 42210 -
obs0.2394 44327 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.6 Å2
Refinement stepCycle: LAST / Resolution: 3.2→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14301 0 19 6 14326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001714645
X-RAY DIFFRACTIONf_angle_d0.455919812
X-RAY DIFFRACTIONf_chiral_restr0.03972071
X-RAY DIFFRACTIONf_plane_restr0.00412590
X-RAY DIFFRACTIONf_dihedral_angle_d10.14245402
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.469137791732
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.483874738158
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS0.10892961049
ens_4d_2DDX-RAY DIFFRACTIONTorsion NCS0.66913540799
ens_5d_2JEX-RAY DIFFRACTIONTorsion NCS0.580673361583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.270.40271570.34532816X-RAY DIFFRACTION99.27
3.27-3.360.35651470.33662802X-RAY DIFFRACTION99.36
3.36-3.450.36521430.31562797X-RAY DIFFRACTION99.22
3.45-3.550.35131300.29342835X-RAY DIFFRACTION99.33
3.55-3.660.38121390.26772838X-RAY DIFFRACTION98.94
3.66-3.790.3481260.27222795X-RAY DIFFRACTION98.28
3.79-3.950.32511280.25292832X-RAY DIFFRACTION99.6
3.95-4.120.27681500.2482813X-RAY DIFFRACTION99.56
4.12-4.340.29661470.22122813X-RAY DIFFRACTION99.46
4.34-4.610.30251470.20532808X-RAY DIFFRACTION99.26
4.61-4.970.25751550.19482826X-RAY DIFFRACTION99.14
4.97-5.470.24251370.20682800X-RAY DIFFRACTION98.39
5.47-6.260.27591470.22922828X-RAY DIFFRACTION99.13
6.26-7.870.2541400.21782820X-RAY DIFFRACTION98.77
7.87-39.720.21351240.1872787X-RAY DIFFRACTION95.44
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.660079110694-0.358541425193-0.8246233884010.4478640989240.701261608841.128153048740.02997025486380.794778844134-0.4851842242341.17773187526-0.53830222668-0.250129649679-0.6378420869730.814528774870.0007703069098761.03544037922-0.296039200551-0.2320367051981.20545393545-0.072085460831.08038787896.221539653356.259959908512.071783446
21.833167640220.8770458957570.4736315497262.479684625551.488816700091.61445652234-0.4024633807080.4862790118710.187306851534-0.04390069871590.1298909063060.0392602793636-0.4618408519590.0567913446039-6.62793321461E-50.802815180334-0.0510629713145-0.08185903302410.7979372184910.0309677110210.75095458852783.914676079448.655014120114.3986864623
30.4788396703191.733633770030.6035113755812.31726281470.6895252739180.144560123074-0.0291085905251-0.0301810055239-0.3281030570110.2219254122310.411375333795-0.09526571162110.100077870930.3695891629939.67808597627E-50.801817096923-0.0748140603376-0.0366103693090.7891988760840.05615048190480.69041705947963.456194321518.242385765210.1932156189
43.208962253712.21712753421-1.427115153812.63481700909-0.6379034024091.67957361853-0.406628162010.216563002074-0.449380674954-0.234168578370.294961225495-0.1953892017110.1286296943880.171081988925-0.0001077145131480.611762823560.02001680283440.05570753705870.8676316040540.02709174279610.69809783946142.140445032-5.9973126282612.3992582931
52.809883418021.10444737908-0.3847116945280.741303797965-0.02884101591890.6838151540530.0648299160917-0.1449102662730.03493338867550.0151662004539-0.15324253369-0.00869115052771-0.08108687633210.206872411168-9.26375487327E-60.700844015672-0.0174118325844-0.03950160284160.8065402858510.0124660388230.67734632758259.871968055934.839852359412.3613052821
61.365954259321.02799971099-0.730623653093.125403142231.637115959571.997002668450.205878269881-0.1605369690960.174555396438-0.0726517242301-0.161720601540.0112934035274-0.265233068318-0.0619816079297-4.89305397884E-50.7006690106050.0242110949669-0.05459112468920.8405312472010.01274314422840.73215893131339.334509112321.274866403316.4977668374
70.717026840687-0.311946907174-0.5841737326860.2174518518450.3039907301150.447906074291-0.861841531583-0.807375638015-0.1300955308740.08877400069880.353073865751-0.551445817616-0.2326735954560.8886205924160.005126587299160.6910784108340.0227368515408-0.1627028484430.822139627180.05483922866670.72241382051741.19606589048.245562222926.7120016163
81.583549940470.788962937596-0.3198020075391.83688484099-0.9422917813180.578466000561-0.0136448199612-0.258669797246-0.1798846218120.1858417485620.0273356593534-0.02633643926360.1002113500080.07251759057090.0001885895060140.612016334544-0.04029257794430.004334700214010.757086697836-0.01432672008460.74146230915225.8569506621-6.8870658155829.2552119478
91.73342197080.3854261849470.7503434839990.2968102841180.4022258440860.5549131130590.23974132824-0.256743761188-0.8527790618920.215196410453-0.0444078588310.172126568473-0.05239369694130.5866617227060.003272029378081.49569673036-0.2300315715390.1745612943211.532267516760.4720301161160.76537476369418.6082958695-33.104902788250.4844474546
100.4024333296890.423542545688-0.2657668857440.483069121443-0.3259029712780.5208288106940.4903338398710.195853956289-0.4712383263580.636083081209-1.381264812990.7355591395820.0535749131985-0.388477352625-0.0003333064906411.360532456570.0917006646179-0.06640134234140.967142971728-0.02039458440621.0495523897220.2465050606-22.550892658151.0061262124
110.4368877101590.468467229778-0.1864386194980.453499535988-0.2027965838490.04900163514890.1069785052370.191671535267-0.2842434774440.0735604440409-0.2287368611330.623263447635-0.1513815842020.4752881903520.0006027059432020.8889712684-0.1427585378210.05964961996441.01802727242-0.02242770691991.0817028273719.6435045604-28.510783867539.9033993822
120.09508817044650.05263178453320.134087802874-0.002922758590590.05787014777980.171640574614-0.193437730586-1.558916590110.3674802384881.45112225281-0.1978780786130.551770455631-0.05824696456710.7189024569440.0006298884119670.957596324839-0.03092844940980.07897849004351.412111970830.1591059276511.3303507945110.2848945558-22.938325061940.326667823
130.3408357591460.3556654279150.4107096334920.835174760270.832022353590.765690795779-0.04894542753250.260273622225-0.145404175770.671772795071-0.2052173051370.262510676271-0.0196154548090.02205826985110.0005985947918580.783537781674-0.042084725321-0.1643457287721.08715839790.09151930499910.80044578054722.5986790651-19.101534792539.0672491032
140.6600011334580.6869622840570.4844926224280.9983583151670.1370667841631.14556887881-0.1792686196840.104475482742-0.7186588150360.614546156491-0.004400589373521.199620807690.1497240378880.1136328676647.88888226483E-51.202113593260.04979142041070.06348161747510.4506869186370.03822489838820.90438738401320.4758592314-20.01532233147.5991126796
151.13767295616-0.3766908895170.9206039694930.244342897343-0.04916641964450.8181979569960.375845484314-0.0224439643776-0.6092739725210.907215287014-0.3895759129031.131206522090.769671271234-0.08693879251240.01117249439221.19208468261-0.1638118711310.2950740880871.023505290020.1179340074011.2496089203815.5239244321-30.464445051742.2156352777
162.736308523280.6593355817411.515196114141.323921360.09461083414132.85014287217-0.0240738544026-0.0108313178853-0.00500410993158-0.064454417942-0.009786689657960.364237059687-0.21284952562.00861722158E-5-5.17491230956E-50.651224707814-0.0425718939743-0.03691985892350.8737006031690.02581257786730.799132356856.31779775423-2.7914674189612.1359580152
171.651495611580.7417513478070.3802121594330.3957306387710.7996687750261.781967187640.130395562110.551646412734-0.2560366651710.04259019210080.0186263588507-0.06579681377770.02538581481050.0471756784654-8.25783950955E-50.5882975183070.0650064406565-0.04844958148860.739666238931-0.09067870096510.8231033159048.01602605425-2.5815012010710.6820886527
180.887461433783-0.0684633389736-0.4854057246811.12882541161.748332282132.27745474247-0.0221740471729-0.4432191964090.162763572536-0.09235065141640.1078445356720.211747099091-0.1823598799660.5914492016777.91634780692E-50.7876748415510.1084734735640.04634252561440.9234120830150.05122546880810.86219087908741.524422634830.7687571853-57.8201294102
191.477303399250.488418271906-1.776408830650.194671184442-0.5413209174372.086118553161.119809717850.3103756560250.02278347929260.497889338605-0.30724774244-0.259436573929-2.05373356686-0.3374730338480.04788228611470.8696968876830.1661468442910.03618600640060.555155264627-0.1264319475230.8028901577641.057799188941.0654051314-50.6597805953
200.422304897786-0.1175604602350.5423508972310.2861884925270.2234200580011.17585326790.4766813434110.3263891689880.2436874977060.494794964556-0.1070538633030.137258566589-0.2506087401340.3414645373044.40961768133E-50.8560630111260.03559197666880.0795445958950.570379457704-0.01080558599610.80418982699138.368847077237.7629856462-59.5542227424
214.055507430211.355782642751.131496514333.71378789969-1.665212592941.54890213209-0.5080689597941.13701665671-0.266884383484-1.189547093680.004572407628770.06349647339881.069314923230.348868445965-0.250159414010.9400010169450.223067126968-0.05737229005340.0645228016909-0.01240440996880.53862617058242.448915924627.6498734846-52.6977396502
220.331726280918-0.394066122509-0.575401337480.1373892287360.2172579538340.3030251610840.269239266508-0.8595072123580.782286368523-0.3478372283210.317588291950.3362116668021.385965744280.8813226708030.2022788743760.8074128734240.0353868636409-0.01021282328450.6224708198550.02278839545170.71822940360744.726282806828.3223441911-56.5123331567
231.37874204716-0.7337840447410.1838699547090.5385731123520.3344535059080.7547693065320.1969071798930.0939946495550.284328237329-1.4021642211-0.802727734432-0.5750345606910.0616822247283-0.0463754180449-0.000126456700520.8504508133630.139383021340.2271350521111.111313586610.006255171140130.95939645841196.2988745554-28.7169952205-12.8740225577
240.784945830424-0.07840641492680.5340938844932.640783413850.7704898634222.09631587289-0.069646187356-0.142342672053-0.322406131105-0.21843861078-0.18620804829-0.06674872121180.2504762436690.15918919231.22332105257E-50.6424778607510.05669963941650.09375257945271.01280718586-0.01007508794210.69406437026784.4452757727-18.2581686293-14.4490176675
251.85051947042-1.83588341074-0.8318018341463.22281965213-0.826202495647-0.3515606906620.06424360107680.3685092741470.05215072721680.173736974106-0.199409175667-0.02915881601770.101986600152-0.207669722078-0.0004289108340980.7557361567890.0336604632804-0.08207316144830.8918835391890.03563460070220.65273825470268.3091882277-1.37959280587-11.9997301105
261.374965756440.1268111345570.4540540517681.174827760490.01995397780860.0373508157529-0.312663285161-0.5680488907610.03008891149180.4398643611230.138275405236-0.1052354942240.3219591910010.3188828358780.0002024820120080.7190447151510.0550980804422-0.01583185717181.007671919410.04062319822780.67276758745747.449878536726.3547642582-12.4137451682
271.36787309391-1.593670419170.1769876856852.46077826660.4154002487461.1985761896-0.392144877331-0.1139700914691.048507597850.1351272152760.419104213446-0.119214885686-0.6718078283650.2509544872510.0001550556360110.827674008350.0168695702255-0.1184871492031.07552819813-0.09507127351410.88717609370736.726086311241.186310161-13.7189702799
282.41842800967-1.210083393491.357891738821.07747614047-1.056714302790.700052809527-0.0727719982189-0.537629071029-0.1005286907210.01194826753490.1211753542520.09491035002360.03063756110620.1632297574086.38940584464E-50.74027960278-0.01816385784130.02886579512030.987958774863-0.03139581401210.67864021988856.792086252-5.96945520376-12.1009542561
292.43835999603-1.572743024670.4770281065283.438740877950.1397412924741.670588216660.0298010090779-0.0129362402065-0.0214512661654-0.160509715343-0.08406112586870.0596827802604-0.14369042152-0.1234180131120.0001265985528890.6093614417980.1072304644940.04196968678180.729208735874-0.0380407313870.65171026977930.234703622529.3383510959-29.1259440002
301.60520510726-0.480981461752-0.4891343864070.7230804941640.2940002313360.1770488949960.002119969189390.4487110116060.696640005007-1.095261626870.4114147647430.7117393174540.8192799772270.1321625940860.005786867721422.026505121350.487453105505-0.2138830570351.12852476291-0.1960336515590.89064743177120.774904618461.696995137-51.8493936032
310.0234675834903-0.004957937912620.01283744191410.0278261467092-0.03968564234970.03158086285540.3390839407780.1072951114280.3778678238250.1635182010770.03061729823251.269916518320.7065001163930.1151765103830.001571979834692.033265845160.1601517453870.05372040026420.797836769007-0.1894498493331.4686622986817.887017935739.4849495136-57.9396466033
321.68407849351-0.423057988035-0.1141752255640.1228517653330.04448709713630.0107032032060.540049130694-0.1234584714650.634133654075-0.458501475535-1.03313890779-0.5079580258290.3864642523130.8002931164070.004435488181581.975993402580.2869347878350.140492492521.503036591280.1725105778130.96887721620825.558033841658.1861189375-49.301704753
330.131689651034-0.160764960019-0.01094057535620.1660391015640.116956749840.197137836885-0.4054256095341.147393755650.67622974726-1.28937361623-0.1175224767481.02786510991-1.37504951895-0.7016019245750.0008534580569341.353124944020.180766320713-0.18781877831.22135885749-0.008917858885441.0836110094620.616270429853.7708511583-39.7544715633
340.266598189646-0.283924042635-0.0948244468940.3663766227290.04731390581640.0682036196372-0.3811658274580.302405819992-0.0598102637105-1.13486819553-0.472632654537-0.230702222666-0.747748197982-0.201276737727-0.0001645570249621.200907964190.1313924508530.136829457981.22692149695-0.077488818811.0688417623122.985633646345.6153122557-42.6730629218
350.09830616109120.0210077618736-0.0279409276177-0.00838874178647-0.009433172762210.01752607933710.605953326227-0.428579153628-0.08869873319880.09775201203320.200302244171-0.549735332687-0.9477358646170.2332532102560.0006276808733281.769338312590.1450108895530.02305349693280.931514532717-0.2163911921081.0187599804828.92787198554.6811343481-48.2375775059
360.509078715110.0536959855252-0.6934809335310.2788581859-0.3851714454491.08592358070.0818847097686-0.0892996621386-0.130059659651-1.64809980961-1.204451875291.78954438341-1.11892287621-0.710124985421-0.004481501547591.644812345870.716576915203-0.3513871068751.3028289582-0.1563208428151.2419915792116.465647298349.8275795735-46.6252445974
370.194226977669-0.0765355270302-0.1407327550980.06087900080610.05517594724050.02939686787390.1012783628620.285839505375-0.305932644275-0.2077420962810.09314259944810.753474484699-0.338101953808-0.3039316021920.07332959884612.036558093050.518572999191-0.3860055521620.527652475946-0.0175584953571.3715106649716.837306911759.0139883972-44.1493350109
380.2129991871670.126151100801-0.06589446992140.0238925872617-0.02768095340660.05890685268430.1778339654530.2611989669840.7843550233010.164156174997-0.4838256118181.14835290302-0.0452355433569-0.661130492872-0.004026345829530.7792378635790.03733684972830.3620963745671.556524651090.02782468381471.47435573601-0.43993547269127.6330816247-9.18310678473
390.0172398706738-0.0905632581962-0.01892417508990.9677563235650.2135696420180.0740456036712-0.321163036689-0.09337868126890.7401984854581.151154331580.1967968168920.747416104119-0.0249835181595-0.1523763893140.07248924797450.991262632910.3782618229150.2029335320281.836557982810.02331929965280.99383162148911.159195037931.8313813405-8.37606693289
400.1457438071050.41793759270.1665390627240.909574816540.4762585883950.1851297337180.153244112733-0.420820216754-0.512524034122-0.340430534253-0.3782820598861.106126186450.6656423417140.225850275152-0.01155769348790.965175946723-0.05704832380410.0455779772491.15306580052-0.1265187513521.131824055627.9610788904925.2547808221-18.8767793272
410.36369113025-0.0392123125914-0.1845761951980.249866923145-0.2191663654970.3346270696230.108853890711-1.399090824590.972823854738-1.11217402693-0.04703812387961.57720347809-0.387802746207-1.72078507783-0.001341474051350.6715088378650.185714206968-0.09805735966681.212737340350.01597919048431.401958063269.2565113672434.7982563566-21.768512771
420.00233355177266-0.09234390830210.1178729109811.5814184578-1.647606253161.65690145170.8063356286840.5849821394450.4385770677730.3747691506930.5889347933380.905681042229-0.79953735139-1.026636350690.07999608715770.5887372662320.1205075415090.1142894578961.52934132232-0.02672580838431.506534492133.0931278149136.3745590073-19.4745675178
430.22345297280.352091228792-0.3494304254682.11267796028-0.0776051013090.572448710547-0.222164800834-1.543167297-0.5675581659270.07514775431850.0752601294421.04548436510.0587423930806-0.293935726164-0.0002986330759050.7737174195210.0488896302779-0.09997084720141.29152518542-0.09809345974761.219694066748.2431977199830.1680204769-15.1953251141
445.594933100521.700371978851.859390075171.569206063312.255250998043.420300938271.425825092560.282980568948-0.2765883781580.2029363286050.06868003873030.3485587277010.8372268688330.2971279978271.278890800760.850442710733-0.423637044440.1420080929830.9464455694680.4204029629570.7398933335225.8423330833623.1068944453-13.1162587565
451.57959011776-0.119927863987-1.0152137311.075081978181.041388931081.46443818293-0.134466048191-0.692032724299-0.09003962766970.5068652918310.184833345897-0.1157447338940.111439255701-0.297074119274-0.0002557280009820.7903766037010.0170384843611-0.1040168579920.984179865852-0.01713387486590.78771658160735.1626520329-2.5932244956262.3539306787
460.309590379233-0.166537490344-0.4448595717750.4109433877610.3837061453870.820306539320.293760496040.3701087961270.3987189971771.12280768909-0.4212533344640.0121849330848-1.11694342196-0.230458173051-0.03419355846980.746353621356-0.0513924219389-0.0231096669260.8840627363950.1843798969740.72447165465836.7110853603-0.50800897898250.4542522173
470.8205877278020.2400187698480.519198212530.08478571595560.2026219961130.508115663937-0.9537611278141.690095068171.44523938625-0.612006598298-0.2933670500880.162437431460.2633370975450.263970325769-0.02739995916530.825813692985-0.08110684011420.0817775596521.503690800420.08554591142650.9477921691152.613331384-2.3077303571859.5246577361
480.09565626120680.08096134953610.04910810124190.05742477797160.03811382316940.0366484607392-0.732298027443-0.497119684744-1.88209375069-0.3052637992480.32066708213-1.225331393640.7770162066561.505703686560.0001638901750340.8427030696220.147581839915-0.1382964133591.070502243910.09552871942210.70569761200741.5068255871-7.7126634084651.3315885863
490.1752989632910.1075215478950.1464288121510.194814434376-0.04183127307170.210828616738-0.428391579820.1350728537030.5530484727020.444338467190.00328795050002-0.4857296764960.8005663933880.245059688555-0.005249990796210.9864484972640.00197473294924-0.1319789382470.999726224503-0.03093694975310.78700303178638.3878698017-12.943356151149.7686444218
501.170955267310.120036757356-1.936889110891.1007353631-1.308799050544.34324279814-0.05601645961230.211555492625-0.879358315363-0.3416634266460.2342372543531.28158594920.699469501484-1.66282902298-0.5701908832120.842840393773-0.1865480749910.001422482339790.450799039855-0.03992658941870.80491852269629.4803793497-6.6418886755753.1809306915
510.186843522983-0.442603080681-0.1491823629721.267734869040.3691553261970.199330690888-0.204773060732-0.391771655340.4689756907860.142590806114-0.051402067846-0.1836294664550.6529304673920.0665735944858-0.3311394098571.09001764542-0.454096470044-0.309020652641-0.175779647929-0.01830609956050.89739049346439.3218274548-11.710265895962.3385655557
520.001358633745680.07999212982050.0971311416864-0.073144862361-0.1161217000750.250699843496-0.244807880783-0.586242926646-0.4841050454480.129598010020.1098809462240.06826497554530.369675300036-0.2107058179680.001269870907210.828783787367-0.1542451330110.1383702875061.06075485930.07847774472150.67134953795239.94311743670.47037501484251.8507652317
530.5274214376791.601946958530.4377321967134.596148253011.223466661510.3356898070670.760344035364-0.15201666024-0.6325356529131.14651450126-0.116850084982-1.182522353340.2867293962411.75828566746-0.1318545489490.723852321728-0.0148732518319-0.04662610448921.52481200642-0.2121092892210.79882596659741.16514402345.240366480443.421805423
540.0597891959946-0.242379297594-0.3399684613280.399452948680.6420148352160.974774992539-0.6373401350610.6935619637720.705373832062-1.275187856950.404450380788-1.21719155826-0.1321601227590.07876719643820.001932425080270.679364143521-0.1212019854260.009126540853210.8267527876020.1685373262050.58124191340642.7522936922-4.5387161646367.5155967649
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 28 )AA5 - 281 - 24
22chain 'A' and (resid 29 through 127 )AA29 - 12725 - 123
33chain 'A' and (resid 128 through 182 )AA128 - 182124 - 178
44chain 'A' and (resid 183 through 291 )AA183 - 291179 - 287
55chain 'B' and (resid 7 through 95 )BB7 - 951 - 89
66chain 'B' and (resid 96 through 143 )BB96 - 14390 - 137
77chain 'B' and (resid 144 through 159 )BB144 - 159138 - 153
88chain 'B' and (resid 160 through 268 )BB160 - 268154 - 262
99chain 'C' and (resid 3 through 12 )CC3 - 121 - 10
1010chain 'C' and (resid 13 through 30 )CC13 - 3011 - 28
1111chain 'C' and (resid 31 through 41 )CC31 - 4129 - 39
1212chain 'C' and (resid 42 through 53 )CC42 - 5340 - 51
1313chain 'C' and (resid 54 through 74 )CC54 - 7452 - 72
1414chain 'C' and (resid 75 through 93 )CC75 - 9373 - 91
1515chain 'C' and (resid 94 through 119 )CC94 - 11992 - 117
1616chain 'D' and (resid 4 through 68 )DD4 - 681 - 65
1717chain 'D' and (resid 69 through 120 )DD69 - 12066 - 117
1818chain 'J' and (resid 3 through 54 )JE3 - 541 - 52
1919chain 'J' and (resid 55 through 68 )JE55 - 6853 - 66
2020chain 'J' and (resid 69 through 92 )JE69 - 9267 - 90
2121chain 'J' and (resid 93 through 103 )JE93 - 10391 - 101
2222chain 'J' and (resid 104 through 123 )JE104 - 123102 - 121
2323chain 'F' and (resid 5 through 28 )FF5 - 281 - 24
2424chain 'F' and (resid 29 through 108 )FF29 - 10825 - 104
2525chain 'F' and (resid 109 through 182 )FF109 - 182105 - 178
2626chain 'F' and (resid 183 through 238 )FF183 - 238179 - 234
2727chain 'F' and (resid 239 through 291 )FF239 - 291235 - 287
2828chain 'G' and (resid 7 through 116 )GG7 - 1161 - 110
2929chain 'G' and (resid 117 through 268 )GG117 - 268111 - 262
3030chain 'H' and (resid 3 through 12 )HH3 - 121 - 10
3131chain 'H' and (resid 13 through 19 )HH13 - 1911 - 17
3232chain 'H' and (resid 20 through 30 )HH20 - 3018 - 28
3333chain 'H' and (resid 31 through 61 )HH31 - 6129 - 55
3434chain 'H' and (resid 62 through 74 )HH62 - 7456 - 68
3535chain 'H' and (resid 75 through 84 )HH75 - 8469 - 78
3636chain 'H' and (resid 85 through 101 )HH85 - 10179 - 95
3737chain 'H' and (resid 102 through 119 )HH102 - 11996 - 113
3838chain 'I' and (resid 4 through 18 )II4 - 181 - 15
3939chain 'I' and (resid 19 through 31 )II19 - 3116 - 28
4040chain 'I' and (resid 32 through 47 )II32 - 4729 - 44
4141chain 'I' and (resid 48 through 61 )II48 - 6145 - 58
4242chain 'I' and (resid 62 through 75 )II62 - 7559 - 72
4343chain 'I' and (resid 76 through 108 )II76 - 10873 - 105
4444chain 'I' and (resid 109 through 120 )II109 - 120106 - 117
4545chain 'E' and (resid 3 through 28 )EJ3 - 281 - 26
4646chain 'E' and (resid 29 through 41 )EJ29 - 4127 - 39
4747chain 'E' and (resid 42 through 47 )EJ42 - 4740 - 45
4848chain 'E' and (resid 48 through 54 )EJ48 - 5446 - 52
4949chain 'E' and (resid 55 through 68 )EJ55 - 6853 - 66
5050chain 'E' and (resid 69 through 78 )EJ69 - 7867 - 76
5151chain 'E' and (resid 79 through 92 )EJ79 - 9277 - 90
5252chain 'E' and (resid 93 through 103 )EJ93 - 10391 - 101
5353chain 'E' and (resid 104 through 112 )EJ104 - 112102 - 110
5454chain 'E' and (resid 113 through 122 )EJ113 - 122111 - 120

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  • 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

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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

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