[English] 日本語
Yorodumi
- PDB-7l6v: Crystal structure of BoNT/A-LC-JPU-A5-JPU-C1-JPU-H7-JPU-D12-ciA-F12 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7l6v
TitleCrystal structure of BoNT/A-LC-JPU-A5-JPU-C1-JPU-H7-JPU-D12-ciA-F12
Components
  • BoNT/A
  • JPU-A5
  • JPU-C1
  • JPU-D12
  • JPU-H7
  • Single-domain antibody VHH ciA-F12
KeywordsANTITOXIN / neurotoxin / enzyme inhibitor
Function / homology
Function and homology information


bontoxilysin / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesClostridium botulinum (bacteria)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsLam, K. / Jin, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Plos Pathog. / Year: 2022
Title: Probing the structure and function of the protease domain of botulinum neurotoxins using single-domain antibodies.
Authors: Lam, K.H. / Tremblay, J.M. / Perry, K. / Ichtchenko, K. / Shoemaker, C.B. / Jin, R.
History
DepositionDec 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BoNT/A
B: JPU-C1
C: JPU-A5
D: JPU-H7
E: Single-domain antibody VHH ciA-F12
F: JPU-D12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9899
Polymers115,7996
Non-polymers1903
Water9,368520
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-67 kcal/mol
Surface area42430 Å2
Unit cell
Length a, b, c (Å)115.899, 157.645, 173.001
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

-
Protein , 2 types, 2 molecules AC

#1: Protein BoNT/A / BoNT/A1 neurotoxin / Bont/A1 / Botulinum neurotoxin type A / Neurotoxin A / Neurotoxin BoNT / ...BoNT/A1 neurotoxin / Bont/A1 / Botulinum neurotoxin type A / Neurotoxin A / Neurotoxin BoNT / Neurotoxin type A / Peptidase M27


Mass: 48551.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria)
Gene: a, A, boNT, bont, bonta, botA, ACP52_06670, GJ703_01514
Production host: Escherichia coli (E. coli) / References: UniProt: Q7B8V4, bontoxilysin
#3: Protein JPU-A5


Mass: 13674.280 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

-
Antibody , 4 types, 4 molecules BDEF

#2: Antibody JPU-C1


Mass: 13297.776 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#4: Antibody JPU-H7


Mass: 13326.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#5: Antibody Single-domain antibody VHH ciA-F12


Mass: 13201.407 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#6: Antibody JPU-D12


Mass: 13747.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 3 types, 523 molecules

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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20 % isopropanol, 0.1 M Na citrate pH 5.6, 20 % PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.01→116.52 Å / Num. obs: 103244 / % possible obs: 98.6 % / Redundancy: 2.8 % / Biso Wilson estimate: 34.82 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.089 / Net I/σ(I): 7.5
Reflection shellResolution: 2.01→2.04 Å / Num. unique obs: 5017 / CC1/2: 0.352

-
Processing

Software
NameVersionClassification
PDB_EXTRACTdata extraction
PHENIX1.19_4092refinement
XDSdata reduction
Cootmodel building
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V0A
Resolution: 2.01→116.52 Å / SU ML: 0.2711 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3387
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2344 5109 4.98 %
Rwork0.1968 97538 -
obs0.1986 102647 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.37 Å2
Refinement stepCycle: LAST / Resolution: 2.01→116.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7965 0 9 520 8494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00638143
X-RAY DIFFRACTIONf_angle_d0.798611026
X-RAY DIFFRACTIONf_chiral_restr0.05291194
X-RAY DIFFRACTIONf_plane_restr0.00451435
X-RAY DIFFRACTIONf_dihedral_angle_d13.07622928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.030.32571490.3332983X-RAY DIFFRACTION90.31
2.03-2.060.34171710.32943056X-RAY DIFFRACTION93.84
2.06-2.080.38721480.31923213X-RAY DIFFRACTION96.22
2.08-2.110.30161680.2963241X-RAY DIFFRACTION98.3
2.11-2.140.32151720.28663256X-RAY DIFFRACTION98.65
2.14-2.170.34091720.2863228X-RAY DIFFRACTION98.98
2.17-2.20.30611670.27353275X-RAY DIFFRACTION98.99
2.2-2.230.31990.26993267X-RAY DIFFRACTION98.92
2.23-2.260.33252040.27423231X-RAY DIFFRACTION98.91
2.26-2.30.3221800.25283257X-RAY DIFFRACTION99.02
2.3-2.340.27241700.24663285X-RAY DIFFRACTION99.34
2.34-2.380.30581640.24453274X-RAY DIFFRACTION98.76
2.38-2.430.281740.24033245X-RAY DIFFRACTION98.47
2.43-2.480.2791670.23123243X-RAY DIFFRACTION97.82
2.48-2.530.27431730.22193275X-RAY DIFFRACTION99.14
2.53-2.590.24721660.21223300X-RAY DIFFRACTION99.34
2.59-2.660.26841900.20733297X-RAY DIFFRACTION99.29
2.66-2.730.25881690.2063290X-RAY DIFFRACTION99.2
2.73-2.810.27481810.19953275X-RAY DIFFRACTION99.25
2.81-2.90.22791710.19933317X-RAY DIFFRACTION98.92
2.9-30.25171810.19883232X-RAY DIFFRACTION98.41
3-3.120.23261540.19613335X-RAY DIFFRACTION98.78
3.12-3.260.24491630.18483210X-RAY DIFFRACTION95.74
3.26-3.440.22191570.17683309X-RAY DIFFRACTION98.72
3.44-3.650.21231560.17933292X-RAY DIFFRACTION98.43
3.65-3.930.19891780.16433289X-RAY DIFFRACTION97.94
3.93-4.330.18621610.15463285X-RAY DIFFRACTION97.26
4.33-4.960.1661710.14573185X-RAY DIFFRACTION94.51
4.96-6.240.1851660.17283312X-RAY DIFFRACTION96.83
6.25-116.520.21031670.18113281X-RAY DIFFRACTION92.22
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)
11.23552034229-0.658972783145-0.5076674533222.51396600884-0.1323951235861.761749515190.0379535570431-0.0835359719743-0.06540701144830.150572242982-0.03390469474980.392001409060.037303238303-0.135596627172-0.009137336119790.2387745529950.01370337733680.04771698151880.2884236583240.03986006320140.317171063767-72.337168253832.389582677538.6394019007
20.94268763088-0.10471177253-0.08974226451311.20719659764-0.1523760166280.5992685786970.008176340360330.0563323905792-0.14507717375-0.03995754559820.03299592093630.2557281324420.03894479207-0.0958208064195-0.04170933988240.254855416302-7.52102774978E-5-0.002884358311170.2770087628620.01940299314090.300246314392-69.159870883728.507125971828.3601931879
31.57656017756-0.7381111752570.3332547108861.58882285895-0.4922489252060.9213086255720.09146739898460.249931516932-0.11365173062-0.24145541888-0.04622307307290.1354976207720.0656147467739-0.023264601317-0.02967302563860.262435606143-0.0152394987073-0.01567544140030.252177118424-0.01385825622910.210863875202-63.738225145231.41616394417.9966386707
41.48789297338-0.2937198459711.656614769160.972681993803-0.5976407440973.46338006489-0.1139149788590.815309876362-0.368206892378-0.3432891160740.2149053444140.7015971093480.270204684697-0.737274817905-0.06300536285310.476558672454-0.112852601834-0.1865789657261.013050078920.09308413905531.57787275382-102.36318863618.065548184114.4098233801
52.72587810658-0.198755770078-0.3327814512252.33641825653-0.1990095158471.686672371280.2117039630250.663137002736-0.637479978697-0.485242427040.1176244244491.00178142270.223334046445-0.733651484172-0.2706326804610.416498267911-0.0264159210932-0.2022728889430.7638923641430.04335307787490.995867560966-95.723281180925.183481225515.1766589896
60.0429080438322-0.2836692280290.000469131958937.49515911732-1.652358359121.576940481780.41633267640.495962919615-0.41175724936-0.325429349645-0.02414329776670.705092777812-0.0156775950937-0.0602238913216-0.4254138087860.5190069683140.0319519493196-0.2202058513910.6846997637620.1589311921341.07990144754-86.07771513413.8601676847912.3335651822
73.194056783121.46106201633-1.417601061174.05454689239-2.675139262193.99025763299-0.0211065710176-0.100369305974-0.5238762124930.15998156783-0.08612950022990.4540015295540.0675253113906-0.5548586618970.1917310688310.596172388-0.140012439193-0.1437472070880.5375184574080.06419013274471.08986045147-88.3959624111-12.532442209521.9532234835
85.37246536991-0.322060439474-0.2902078409134.162862529980.5702591855383.834091861780.260292869797-0.102888669933-0.495387955822-0.113430687683-0.27971918390.906619910664-0.357486839559-0.413611037701-0.03623544091840.412533007777-0.00441179218451-0.1049920426230.3622211567640.02596066547570.76772791806-80.60674334470.33673267945120.8667589936
94.009619829191.445073606140.3302140500272.35218973954-0.3546845770742.66013550811-0.017149279037-0.1732489939820.5083264431310.2210024353790.01173891241270.904406750962-0.178516884967-0.377414173351-0.09601869445870.3615384704090.0201418577121-0.001513941586290.343319693172-0.0355672939210.753894380295-79.3490018571-2.1229563741529.2966113075
102.004252573121.116496084470.4494653555697.39176176563-2.697050947194.389737412790.485965344876-0.6998813025920.6296938583231.119930006460.2495314514110.893146924651-0.0668540950372-0.685004839795-0.7130598023350.655310694466-0.04170509474450.08029288799810.6520950775510.07602247652690.789299962868-80.2304183615-9.8128629724835.687775316
111.36657917238-0.2013018287230.8190385131952.38606505303-0.5954306251221.02146049992-0.0182811150422-0.191907737338-0.1281683231520.114068975920.171493190320.866217604043-0.0625985409122-0.276354803643-0.1734666142650.4197542389310.0318062904117-0.02065529759510.4062357293630.0349029973760.785794216048-79.9832230124-2.8854260659623.0886849911
124.60535948735.11215229472-1.420530660977.64123148758-1.617599854512.00330081879-0.491232914645-0.0643677782361-0.161126247073-0.354708920640.4021703278141.216950695480.281015591299-0.6502525638510.1194825747330.385744586423-0.00593438561243-0.07134902409880.6034401860540.1210795671351.03632730814-90.6220746224-3.2372584872823.9889842916
134.702127253281.27242169691-2.588308819081.93825135162-0.249846022341.550338227740.0514568439183-0.910229703406-0.3875685636490.378835838955-0.424318052194-0.1979211956-0.16520762350.7998530897080.3378553600030.39264615335-0.0629721740822-0.03120545205440.4835413501750.02415635246540.385956004312-45.342909632547.710649549723.6279169627
140.0270848893662-0.220614677511-0.0502915287915.27926945448-3.468282250745.26585331701-0.1897060123880.4567429662040.4201511417780.0526046811243-0.122235154378-0.395679162095-0.4675646461480.4516231954070.255273805380.486881353668-0.130171492159-0.03023200487360.633122721540.2476518991120.607427092572-30.802019541165.9719560357.30110552158
152.112359209720.8023994394590.3769692915182.55983513881-0.3910247417181.31047587226-0.1430757234280.2429681569250.0278240595759-0.207791212686-0.02146938850190.0180020330221-0.06798959140390.0837237822140.1462383036230.367605216318-0.0241082992575-0.003312322833030.3408548389220.02266532371310.270031294111-46.798686507952.040558531712.2457805782
163.295212786430.7684445190410.8614973725621.966233798290.8270391318143.9588919983-0.285545220161-0.2835185852940.8021888831560.2554294407870.1032889885770.153291702728-0.56397276046-0.1180996918440.1141552080260.5485476624550.00607193596697-0.02486096672740.355442163052-0.02171590122150.480587636003-48.85938480364.853329538213.541152598
173.51796024977-0.6750544292340.04105622295858.08214618571-0.5777868606765.667841350830.08686373140480.669701223230.03855229329190.0350385454876-0.135075812210.51326211899-0.343653649578-0.6470656836040.1157870571810.496208845395-0.0858474159281-0.05364818660740.5076814745480.0324710326890.292587891101-52.219098615652.03803625121.55513381052
189.91817593867-2.92012303742-3.32716605252.76085748503-1.724347823564.974828028540.02880658001640.2756904444740.1880148093020.776441259106-0.0665288365310.0948010554982-0.648498085658-0.09165599277330.1649753571970.64825773188-0.0741939991419-0.1029625849420.4503804815830.2187296879390.538648641305-45.519788273665.66244061770.905984599685
191.517910438290.4542733014280.3267401294164.96667319165-0.7256959406831.72047582233-0.02294663533480.241779563779-0.146295219103-0.452173108286-0.0763092616565-0.3907304425050.1275868959260.4322365444070.1148297710830.403939226841-0.0320199452009-0.01576511574610.3773157665450.03321094180260.292787843922-42.977576079450.86324314956.11874440124
201.50018684930.6965830381520.09200374790772.47850783252-0.5964631188260.744932215143-0.03511032077620.1953658227870.511778159549-0.05214768091580.01532783191770.0119189429513-0.4027068851590.170696641740.02743873276690.389956324905-0.0510452640935-0.01831699015220.3205468504210.03474106346130.250280280132-48.17301564157.852361468513.9644965878
213.0802493118-0.02425556194640.09132172266014.31022886422-0.005910168372414.25770427821-0.0422180654176-0.1102185276730.6773271586920.126296987419-0.552946892114-0.31708455024-0.8118383349010.6920623289530.667050346770.537161635629-0.189842033662-0.08013049263020.47195944050.04934610229840.571764286063-34.067718935866.867070662313.3193400777
227.0286505793-0.8697461071210.980421430396.28934325045-0.04160517944298.79976975484-0.2549459774580.0249454356940.970935387491-0.007284489772430.379430421877-0.184079723235-1.113787346710.391582632973-0.07286194708180.394962905463-0.04655435180810.01720951526780.380880683292-0.07546746027750.458318412023-88.075624557845.813016475259.5624932248
231.40199849189-0.222443741615-0.02015430707712.6183024947-0.08132004044921.78709300881-0.0444112962851-0.224608380169-0.1063763137920.320173247297-0.0269988582725-0.122196269935-0.03906300387910.1066897954350.08451769643070.2413816354130.02431663678960.009886345422210.358843150032-0.004173888870090.225442936735-89.569217501434.15504130761.6952865367
241.82177203351.7441949031-0.7584263791243.032406934790.9551236573233.264439667790.234584763785-0.901857824409-0.3111027011420.2062097127240.288544543549-0.4923776831780.1901177095210.60464751889-0.6178562074680.2810083109850.0379677495495-0.02165945602790.61853200359-0.02355840761930.357264762336-77.636153632333.27873578962.9635936907
252.44316794455-0.38674418550.8224917609121.15254241414-0.1355122278642.238822088170.0228518475298-0.281803870638-0.133546936084-0.1145853226550.0263739882946-0.1394133551970.21774555037-0.12048860053-0.03463781179630.34354512451-0.0007758695329840.07603293612740.359735730462-0.006352137730080.349348109035-83.428014596630.010442217352.4819544146
262.23316092617-1.293144869551.355030633364.92142736039-1.662875239363.15864983198-0.124595353111-0.0709940900969-0.192376374776-0.04656129819380.138499059785-0.1082067683060.199921946935-0.099563189455-0.05157775670490.3188786666430.01985873390370.03215718787130.3275861546060.04032106297430.307166501807-90.217772203929.666388674957.5623945749
270.9412286555070.939982090868-0.4322342997932.90602724285-1.134074231231.48924422603-0.143041931032-0.362082033272-0.254355812670.0555156206458-0.023072841878-0.6677103982980.1470635358830.3290794646380.1995850531560.3538406576720.0714068166582-0.03567354681130.4761888862890.008923944973610.436733211966-82.025233636528.249828984765.9379483481
284.087388098332.503865531092.292971289752.013879135920.1653180550444.48215876648-0.0232694833352-0.10548556763-0.166972873606-0.02329274966170.0977092243862-0.0815721686987-0.3147679136490.111531052125-0.1333929860490.3548622777010.01753954667020.0772363245190.361060115439-0.003743879527840.397315602792-75.998732196338.075395606353.9050650731
292.255371959880.507930109028-0.8156632328962.27036426966-0.3741951871942.06322928938-0.0195269405473-0.356838721168-0.02322326809480.273509716472-0.050674366996-0.288816941909-0.01717813710510.366547019312-0.02873214608650.3758104031930.043455020742-0.03354939508780.542656468579-0.004679327899250.356144940992-82.253627122534.702054308168.2021714442
306.123980120990.0130050670456-0.1113356496397.08707728971.767598865183.67053023901-0.126551964425-1.06983788648-0.04205450447390.7041413028870.2942597598380.03163751281350.5300303705650.476158476467-0.1567514169730.715445219432-0.00846199411713-0.005348700986480.5867615673130.02391327447310.529282701491-63.147163838959.135647250939.1897737719
311.34315481144-1.315532041590.94995891382.83069133016-2.001260242784.573922079150.399820142346-0.02414029014340.753329271757-0.561392729618-0.22619090946-0.484783789999-0.9459015711650.13484804126-0.1941399973350.825207006553-0.0465145866080.08144244300760.318757866047-0.02487484625780.715254667359-62.992565276382.124048662630.3038087612
322.26059979182-1.678248156421.246206062812.80946333455-2.707853334682.719651635440.4002551119880.1204070037670.134044091689-0.235149915974-0.314886415641-0.3059294414470.2968556786380.384487236947-0.06799978529760.5418532356290.03923031808370.04250086932350.405273433712-0.097225332440.684865379992-60.891440310366.682872246531.6304101704
331.60903477195-0.3249114122640.07502344911274.0642788483-0.03684199280211.480979532230.0697229341389-0.1162986198630.5315991015880.5283534610090.1940865439390.0399896887062-0.3049915502930.00269057078073-0.2026302347740.4817723105460.02443970362460.1202058770470.344768497256-0.01018992482960.471564820026-67.932260672259.404816293730.1999246177
342.83788680938-3.44136347117-2.625297687816.823512324275.695206764837.979986660190.0682168417834-0.6940532855420.883631182920.336278333330.100403372361.37947990527-0.389633835158-0.243267631305-0.2121309497660.6741205093130.07011931565130.2917464151260.490212641367-0.01696878056560.905838609075-76.353128341170.116142165230.6712044693
353.12473040903-1.815268339330.2764577444767.49247837064-1.408139984572.936822318690.1243547425130.2948812664950.958103680103-0.7514554627040.211650741366-0.0487345916427-0.157577268122-0.620462836153-0.2890370566380.5713491021140.04045901794850.05372789814130.3899995080480.1146561620310.570111535067-70.716244832964.432964793619.8193443544
361.045610817690.276158801233-0.3586495069053.086339224870.8096307279752.363549462770.391328648860.09422459433820.261691373252-0.4604606614250.03175388300580.0675687986481-0.498500103126-0.187420874603-0.4507116995850.5799180519050.01037828905970.09496492547140.3676520577360.08166811621630.609140820757-64.559276355570.257691050325.1900144897
371.184194891150.392775278074-0.1705861371022.15009114221-0.2469491875040.4111510470320.150552497568-0.100043115230.7359336329270.2732576410790.03529582874390.283743799994-0.351339823914-0.107411920432-0.206176932820.4845058073310.08713754145070.09108872986890.3807031058240.004782863933120.540754193367-74.40740526860.984605772829.7694355317
382.043756502132.270916537150.3435108838627.04001885787-0.1609987803211.446010367970.320965185609-0.3072399731750.4462494887261.04889948404-0.2795178896980.0493308533073-0.498420313093-0.140058784893-0.0342814202680.7223390169630.05591950359110.143760785350.385616539163-0.1001015587160.626193770241-69.72377723569.425015930435.9788536008
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 61 )AA0 - 611 - 62
22chain 'A' and (resid 62 through 216 )AA62 - 21663 - 217
33chain 'A' and (resid 217 through 420 )AA217 - 420218 - 418
44chain 'B' and (resid 1 through 25 )BD1 - 251 - 25
55chain 'B' and (resid 26 through 115 )BD26 - 11526 - 115
66chain 'C' and (resid -3 through 7 )CE-3 - 71 - 11
77chain 'C' and (resid 8 through 25 )CE8 - 2512 - 29
88chain 'C' and (resid 26 through 40 )CE26 - 4030 - 44
99chain 'C' and (resid 41 through 59 )CE41 - 5945 - 63
1010chain 'C' and (resid 60 through 66 )CE60 - 6664 - 70
1111chain 'C' and (resid 67 through 108 )CE67 - 10871 - 112
1212chain 'C' and (resid 109 through 122 )CE109 - 122113 - 126
1313chain 'D' and (resid -4 through 8 )DF-4 - 81 - 13
1414chain 'D' and (resid 9 through 17 )DF9 - 1714 - 22
1515chain 'D' and (resid 18 through 39 )DF18 - 3923 - 44
1616chain 'D' and (resid 40 through 51 )DF40 - 5145 - 56
1717chain 'D' and (resid 52 through 59 )DF52 - 5957 - 64
1818chain 'D' and (resid 60 through 66 )DF60 - 6665 - 71
1919chain 'D' and (resid 67 through 82 )DF67 - 8272 - 87
2020chain 'D' and (resid 83 through 110 )DF83 - 11088 - 115
2121chain 'D' and (resid 111 through 117 )DF111 - 117116 - 122
2222chain 'E' and (resid -1 through 7 )EG-1 - 71 - 9
2323chain 'E' and (resid 8 through 33 )EG8 - 3310 - 35
2424chain 'E' and (resid 34 through 44 )EG34 - 4436 - 46
2525chain 'E' and (resid 45 through 59 )EG45 - 5947 - 61
2626chain 'E' and (resid 60 through 81 )EG60 - 8162 - 83
2727chain 'E' and (resid 82 through 97 )EG82 - 9784 - 99
2828chain 'E' and (resid 98 through 107 )EG98 - 107100 - 109
2929chain 'E' and (resid 108 through 120 )EG108 - 120110 - 122
3030chain 'F' and (resid 0 through 7 )FH0 - 71 - 8
3131chain 'F' and (resid 8 through 17 )FH8 - 179 - 18
3232chain 'F' and (resid 18 through 25 )FH18 - 2519 - 26
3333chain 'F' and (resid 26 through 39 )FH26 - 3927 - 40
3434chain 'F' and (resid 40 through 51 )FH40 - 5141 - 52
3535chain 'F' and (resid 52 through 63 )FH52 - 6353 - 64
3636chain 'F' and (resid 64 through 90 )FH64 - 9065 - 91
3737chain 'F' and (resid 91 through 111 )FH91 - 11192 - 112
3838chain 'F' and (resid 112 through 125 )FH112 - 125113 - 126

+
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