[English] 日本語
Yorodumi
- PDB-6ui1: Crystal structure of BoNT/A-LCHn domain in complex with VHH ciA-D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ui1
TitleCrystal structure of BoNT/A-LCHn domain in complex with VHH ciA-D12, ciA-B5, and ciA-H7
Components
  • BoNT/A
  • ciA-B5
  • ciA-D12
  • ciA-H7
KeywordsTOXIN/ANTITOXIN / Botulinum neurotoxin (BoNT) / VHH / receptor-binding domain / TOXIN / ANTITOXIN / TOXIN-ANTITOXIN complex
Function / homology
Function and homology information


bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / zinc ion binding ...bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane
Similarity search - Function
Clostridium botulinum neurotoxin B, "coiled-coil" domain / Clostridium botulinum neurotoxin b, "coiled-coil" domain / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / 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 botulinum neurotoxin B, "coiled-coil" domain / Clostridium botulinum neurotoxin b, "coiled-coil" domain / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Botulinum neurotoxin type A / BoNT/A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.20000858936 Å
AuthorsLam, K. / Jin, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Cell Rep / Year: 2020
Title: Structural Insights into Rational Design of Single-Domain Antibody-Based Antitoxins against Botulinum Neurotoxins
Authors: Lam, K. / Tremblay, J.M. / Vazquez-Cintron, E. / Perry, K. / Ondeck, C. / Webb, R. / McNutt, P.M. / Shoemaker, C.B. / Jin, R.
History
DepositionSep 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BoNT/A
B: ciA-H7
C: ciA-D12
D: ciA-B5


Theoretical massNumber of molelcules
Total (without water)141,7554
Polymers141,7554
Non-polymers00
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-15 kcal/mol
Surface area49380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.04, 89.36, 143.69
Angle α, β, γ (deg.)90.0, 118.93, 90.0
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

-
Components

#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: 100030.023 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, ACP52_06670 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7B8V4, UniProt: P0DPI1*PLUS, bontoxilysin
#2: Antibody ciA-H7


Mass: 13133.512 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)
#3: Antibody ciA-D12


Mass: 14404.154 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: Protein ciA-B5


Mass: 14186.932 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 11 % PEG 20,000 and 0.1 M sodium cacodylate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 2.2→37.74 Å / Num. obs: 75271 / % possible obs: 95 % / Redundancy: 2.6 % / Biso Wilson estimate: 29.5981913921 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.049 / Rrim(I) all: 0.069 / Net I/σ(I): 10.2
Reflection shellResolution: 2.2→2.25 Å / Rmerge(I) obs: 0.208 / Num. unique obs: 4576 / CC1/2: 0.965 / Rpim(I) all: 0.207

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIX1.9_1692refinement
Blu-Icedata collection
SCALAdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V0A
Resolution: 2.20000858936→37.1635590417 Å / SU ML: 0.233539670702 / Cross valid method: FREE R-VALUE / σ(F): 1.33647799258 / Phase error: 22.8444478048
RfactorNum. reflection% reflection
Rfree0.228599973817 3774 5.01608229884 %
Rwork0.180585060409 --
obs0.182987256077 75238 94.7832550171 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.9171563415 Å2
Refinement stepCycle: LAST / Resolution: 2.20000858936→37.1635590417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9564 0 0 524 10088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008489196766199769
X-RAY DIFFRACTIONf_angle_d1.0875066326613228
X-RAY DIFFRACTIONf_chiral_restr0.04592758542071459
X-RAY DIFFRACTIONf_plane_restr0.004712043378831707
X-RAY DIFFRACTIONf_dihedral_angle_d13.80501766313573
LS refinement shellResolution: 2.20000858936→2.2279 Å
RfactorNum. reflection% reflection
Rfree0.274725339152 145 -
Rwork0.217003227929 2721 -
obs--97.5825672455 %
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)
11.535023440630.05612071847680.382751877750.9944983867660.1734766402910.740870239770.00146797978230.189642089509-0.0747119078867-0.1270055630710.0948877737814-0.04515525127770.1676555952310.1309629757250.003405818320160.2867426643530.006171160899570.0380661167090.191359838175-0.009070637672510.14905435246-31.6178022619-42.547310925319.6305463822
20.906241422566-0.2263067104310.09647223830590.659998828393-0.6257659231120.884232534443-0.07310294531660.02159207086420.0573257014073-0.07580727259540.0828100255527-0.0532577530438-0.0384050341250.1027300674360.002952989296310.1967677533190.01384692619680.02874535227470.190098572087-0.01336162551130.18173771872-30.1291436365-33.529285338323.6758595563
30.3076128622030.04891694220110.3358037438930.322575296501-0.1978900953280.339327398234-0.1349738979710.07754053959460.180674828971-0.09196619248680.0917251997442-0.0709442027673-0.03258737975490.198605049642.15287066919E-70.234752414123-0.01895300638140.01500097131650.251267346824-0.001325594120260.286867275042-29.9721564257-14.85486236222.5020400388
40.897668312122-0.2147691997320.5034188271880.771584918754-0.315501683510.860568610081-0.0479726749725-0.0294224564340.07922928957140.02036623769170.06304440807060.04432322309270.0249965267965-0.07751139678027.38761284026E-60.181695821540.007323778338080.03592908067640.1795421436730.004440741275010.146642301824-38.6829354758-30.375950123129.1564534224
50.607272177943-0.333074995439-0.3160915373970.7776973739480.2804471484040.604932523633-0.03983982744220.2516031431820.0857716294566-0.0872650472504-0.0363106555456-0.0352174827328-0.1458889919220.0159416366113-0.001170363933610.305830905697-0.0427116724523-0.0002474822573020.2988860636670.04518773358510.324268043431-19.7913755033-7.203183533323.2544336278
60.4526129637520.006118031243040.7645780565290.212272986840.4420891616680.721275114804-0.1106875906090.1415501078220.0580574243517-0.2444231050250.1162609013950.05811170445680.00548891759458-0.132114347331-0.003654568357440.3897913368560.007919463720340.04916288904560.2748764357840.02844756722750.315680115589-36.3551053758-28.383427977821.6259743067
70.7331742466550.2630555727710.05423531890350.681603737946-0.5732713805630.812667698699-0.01464203278680.1333364513670.004006929777850.0756019946268-0.120963385885-0.166896370662-0.08635639045590.350717759327.47329929367E-80.226321643235-0.04324851665320.01796572620640.303498698960.0364871501640.3591311362053.29227690724-9.7638383257439.3888374528
80.6447151322620.189002272587-0.3230031612820.7320491625240.3951935371440.893177382512-0.06355512185710.02269818127890.5084241944030.0940222809372-0.165941341062-0.223202659569-0.340736585481-0.124928501694-0.002546581284830.248001713901-0.0171044341521-0.01655866700650.295901820384-0.01648695771880.343979182917-7.6686681846-6.4872756896850.0830073928
90.562226272644-0.593872106874-0.4548743708930.8471702828450.2993442454250.3227137252250.155837698370.2540129995450.1412573267050.110491211418-0.100954720873-0.0419765714056-0.01247566267520.0140248235974-0.0001693029193750.3851173796270.00900662572004-0.02670972930710.2998040530890.00157929843490.386671808585-41.63036065021.7499242206833.5208567259
100.4388186209750.3164669504350.1050498758281.109483274170.1588640434420.5953185366930.0278213343721-0.0140058191754-0.1894223835010.00789427358639-0.08110870271790.0332087173536-0.01670216743240.0665431307326-7.37113373845E-80.222447550135-0.0202483049780.02389738878930.2590443961240.01639455568830.268734761997-7.41848550605-16.468062647345.7034912827
110.9446839929860.795446516159-0.4765015322351.678998888850.03197209774041.17151306573-0.309888684913-0.2628118749060.2520043454850.5875579353180.103160812159-0.16001448220.0760495622306-0.0406158687504-4.40100378032E-80.4042810559820.02919392514010.02031850004170.350734610111-0.04611900226370.407108002336-51.26457977295.1102601391338.3347839787
120.1487951865770.3741802829930.1405683817230.9712806950680.3484887427540.128734374889-0.151908493771-0.08140029987910.1076727367040.147036068175-0.1552230776550.807577441026-0.0377470662981-0.449590976059-0.1051930406220.4443305003450.0522502656056-0.1033490008910.4577872139520.116808377590.469521649716-59.7256054681-7.67365288826.52592569899
130.376787671991-0.300688090614-0.1730648249340.3242975997350.1365118864440.08737493879390.01865383847720.0702662737749-0.361136152471-0.220731894297-0.1450371611490.321103923858-0.0206895738725-0.216934396297-0.004583463818640.566418593894-0.0246486391031-0.02245128169420.3800476358640.06716528890890.335258352759-49.0112185252-15.0656200663-13.3159491217
140.092637290490.04847681195490.06655133914230.03658713880360.01680648767440.0537710735193-0.2514723527830.3017560222580.295155109094-0.1993959553980.2535674928130.156400531143-0.381420787851-0.0113092808797-1.60107417841E-50.469820974916-0.0163628189139-0.06012925000430.3319627238960.06276566664010.251782153517-52.0457323565-7.322781025510.642623500519
150.00503618130979-0.0103720781772-0.003520273533060.0146747896986-0.007880879304130.01353351289190.0227607427255-0.2575397082330.2207615461850.127489860904-0.3367277948780.294633202084-0.872418530694-0.2656719718458.17855767838E-60.5371851916860.112929320347-0.1062350564050.3414958499830.05758881668770.411337291641-51.046050543-5.6879432357615.1632473679
160.355542393646-0.273888202714-0.04206501301290.358237717614-0.2487778016120.325241427277-0.1212658641440.2122844733810.138463459722-0.261390556650.202434740610.1857257975470.0590418483805-0.112579419444-1.67407417117E-70.323857409156-0.0474548893351-0.04781822054860.2777759837480.06932220318460.20082407249-48.4231655595-19.20985541685.00414871897
170.2194112388750.15281848340.1406705783940.184409098118-0.053034883110.238426025099-0.1575175398010.01874826827470.0865409501325-0.1818418325090.304694992361-0.113823421073-0.2834760079860.0959362428782-4.50292697868E-70.445973023462-0.0257556888991-0.01763333609190.3123246403330.0616364728630.278720531564-44.4860787094-11.10167033331.91887404146
180.1008205964520.0727858570148-0.001987500578480.177586136536-0.1062534236170.13246200967-0.173363706030.0662563641413-0.00406257250824-0.2925507341930.1490505696820.06254564579030.12216657433-0.08554384974850.001463245799520.440337696145-0.0699340435769-0.04963188887370.2689063019050.07866193111670.238599015775-49.9238060497-19.0598880655-3.01358481874
190.1151155049320.04753803743570.1744673310450.1035639329980.09987383504620.258298190571-0.131688057794-0.1724972793690.151529877072-0.2280248359970.01225616418360.38777073789-0.101976724871-0.493880251867-0.01504260024350.3454561768170.0296685973424-0.0480999917140.3495084562430.08067096600760.319030686328-57.2655354-14.439298713410.7881502612
200.09063611121060.0386180584070.02561798076920.0628370915661-0.04655410597610.07029723937810.01721263010430.329982580931-0.0654381082022-0.735693195947-0.0376722626644-0.2365374914350.3033275481540.12670688337-0.008742275210040.584226317362-0.0592229852396-0.07015595833420.399161880777-0.002165380233950.303435194385-53.6341245399-18.5909283496-11.0104250121
210.1046478028770.2015429032660.1113303708390.4141365827440.1166772265770.180432540689-0.0352665086361-0.0814368096141-0.0002466456066810.2973475862-0.05959823876940.0386310092176-0.246226689785-0.3483912828860.00317543047630.3290174645950.0678073779433-0.01803713065770.5003422953580.04310988452440.385490798707-10.9054271654-54.787024648158.6827447247
220.0662793941103-0.056064602261-0.03233398909230.1596046782620.1518936511160.128467624245-0.4794355050480.00566175980762-0.5621876309690.1140494961030.2664343618740.2768950102680.045629854569-0.459122738161-0.0003323750353010.3437790610980.0124129563674-0.009124032478950.5436435425190.1172720480930.412398267798-23.414257181-59.418032677156.6714306857
230.122709955637-0.1272349617340.1005634155720.13877505291-0.0703913807620.285871619856-0.0280302308422-0.1230094924350.03016323809520.0432646470980.066222009515-0.0381371625351-0.01983766409150.137132744114-9.52466919125E-100.3040532892530.0488942814256-0.04003756644080.2738044244250.0433167869160.31094380757-14.9759114221-51.443438860347.8830209235
240.352903354992-0.4797425027590.09225527407350.481424202093-0.009815287488050.348843812694-0.0642245955414-0.0696367318273-0.470039200086-0.2010918044330.09035278792440.2788330462280.441884772701-0.0464835795566-5.60674294195E-50.3032576641150.0737354861559-0.05289429007620.3949404817270.05519935902820.380016861362-16.3053045651-63.375223186849.6827508315
250.105158487353-0.06144614111750.1672481310350.194988921996-0.0842254348610.140699968497-0.05250983805250.47332554830.01311315274120.101835301210.0240672669346-0.1761537994310.05059228655280.224925714282-1.13382708944E-60.2854011647050.058169527033-0.04889811181030.3502095197410.01004740993110.329883900397-9.4771352375-54.250545672150.7027652939
260.3957757936960.3208457543890.3457958766690.3094248843660.2393106644880.344465174284-0.0669998760123-0.416342551409-0.259534287321-0.9271540207860.04939306134090.265487217564-0.0104267318854-0.3412404525880.003434761152270.3691323007690.03984896582310.006366914526110.316716568482-0.003004211868360.301038230758-31.0370837773-51.895141169842.0047025356
270.07677363943010.18515308712-0.05914190450030.377828708309-0.2418721417290.2395032612240.0692130444438-0.2596411687680.3213944276750.229027948587-0.00881875369788-0.0158150368313-0.0467587409392-0.0905707015351-1.84936944988E-80.3133550825880.0856351744227-0.0007184137489660.3588261257390.01436186702690.3148793834-17.6126690834-49.018913519753.1883777972
280.04429368803260.0492319649332-0.01428981392840.0332141149845-0.0130472146161-0.0165327635528-0.0943522647606-0.0945928921915-0.09046746253770.09608141032070.0580475316443-0.2708215130490.1104095340850.0826321554363-7.64240575359E-60.486505125438-0.05069925207390.003944387122260.302999156690.0601720496470.381554001079-6.65159298788-37.247453893772.2462423408
290.04432949990980.0002351018269130.05853765895590.153457223489-0.07116513571820.0903939721364-0.146853587158-0.0161635648131-0.09520615554070.307798960932-0.0773696633624-0.129112642156-0.0264734216660.1802128135988.23766208063E-60.339601630121-0.0479408730972-0.01857929068630.4006303552860.007655896425870.246579196688-11.1283474252-31.772700895276.0095515736
30-0.000564038709074-0.00761563187357-0.005623262158350.01440491426710.01506578324720.0281641829479-0.466352477829-0.198560908214-0.3776460131990.124828884396-0.1752004584550.07265876381330.2633344821250.2318987903357.19887454602E-60.3993389504110.0413418673581-0.01455814908130.4102402714850.02763900699410.58413852345212.4553024414-32.731062309365.7492419135
310.147434185265-0.0806316181662-0.03861087714120.04010682960760.06797189211340.0135876919788-0.1555401617790.0802635408301-0.1125929328050.2005147987950.15131145849-0.1871803308930.184212468020.106272940925-7.90359529366E-80.239804022789-0.0746196651756-0.02072981795680.36817533974-0.02065583524050.375006635931-2.4395519579-28.195467337364.9425810384
320.102918626859-0.0707023887050.05345657595350.0331724066987-0.03561234470660.15389309025-0.0402867424168-0.0795360029562-0.0180203053388-0.130500102144-0.06040848501460.167697848903-0.05938974573660.1028870776513.5728323492E-70.300312677373-0.114964784642-0.009181161324910.3936267215890.01587517155860.289963412635-9.59704785285-25.340829798262.685379858
330.1530310368330.0223976639222-0.1541790570180.2186044071740.101802918080.174446086321-0.2050958994530.1060530571370.2468245518070.3056223475860.01388046835110.138204589158-0.4764946664840.1716521603492.08072133599E-60.264620781577-0.0116788615619-0.002164264977770.3709779220970.0426677154590.354714505565-10.9443258194-22.309261384470.7265055166
340.2287932348830.204633960618-0.2241226394850.576968479009-0.06199937105860.2217844534220.0377513940044-0.1074753226080.08006101809720.359153246425-0.198343542786-0.07983525846670.07074699160890.001329169444341.38361927191E-70.374268298464-0.0916679293323-0.01252125373680.3620659281620.008806175909630.307833757952-9.51120203431-29.813804364571.1582082286
350.0832445342511-0.103104476657-0.0432642134260.09306670504180.06038538538240.0621412553439-0.152023094028-0.0521294762114-0.4793995256350.4353437494840.1310978581760.04943591581720.06690712813580.139527006218-1.96883903972E-70.23531910063-0.0469589812912-0.003829716252320.3281357351560.05625270418590.416571024741-0.0481925216974-32.465566199260.3209666047
360.0420480444437-0.05562665215430.05363585768060.0983662667099-0.07330546666390.05493494530440.0311551861503-0.438965929192-0.2308065786510.06561678485530.07550680828210.628179411610.435351758023-0.12553132115-8.86754210088E-70.373686887822-0.06710718431740.05495907691510.462927330780.0919397289480.463710349428-22.0952531702-38.568321532773.8360444406
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 138 )
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 232 )
3X-RAY DIFFRACTION3chain 'A' and (resid 233 through 275 )
4X-RAY DIFFRACTION4chain 'A' and (resid 276 through 416 )
5X-RAY DIFFRACTION5chain 'A' and (resid 417 through 485 )
6X-RAY DIFFRACTION6chain 'A' and (resid 486 through 546 )
7X-RAY DIFFRACTION7chain 'A' and (resid 547 through 599 )
8X-RAY DIFFRACTION8chain 'A' and (resid 600 through 648 )
9X-RAY DIFFRACTION9chain 'A' and (resid 649 through 720 )
10X-RAY DIFFRACTION10chain 'A' and (resid 721 through 799 )
11X-RAY DIFFRACTION11chain 'A' and (resid 800 through 866 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 7 )
13X-RAY DIFFRACTION13chain 'B' and (resid 8 through 17 )
14X-RAY DIFFRACTION14chain 'B' and (resid 18 through 25 )
15X-RAY DIFFRACTION15chain 'B' and (resid 26 through 33 )
16X-RAY DIFFRACTION16chain 'B' and (resid 34 through 59 )
17X-RAY DIFFRACTION17chain 'B' and (resid 60 through 82 )
18X-RAY DIFFRACTION18chain 'B' and (resid 83 through 97 )
19X-RAY DIFFRACTION19chain 'B' and (resid 98 through 107 )
20X-RAY DIFFRACTION20chain 'B' and (resid 108 through 114 )
21X-RAY DIFFRACTION21chain 'C' and (resid 1 through 17 )
22X-RAY DIFFRACTION22chain 'C' and (resid 18 through 32 )
23X-RAY DIFFRACTION23chain 'C' and (resid 33 through 51 )
24X-RAY DIFFRACTION24chain 'C' and (resid 52 through 82 )
25X-RAY DIFFRACTION25chain 'C' and (resid 83 through 98 )
26X-RAY DIFFRACTION26chain 'C' and (resid 99 through 108 )
27X-RAY DIFFRACTION27chain 'C' and (resid 109 through 123 )
28X-RAY DIFFRACTION28chain 'D' and (resid 3 through 12 )
29X-RAY DIFFRACTION29chain 'D' and (resid 13 through 24 )
30X-RAY DIFFRACTION30chain 'D' and (resid 25 through 34 )
31X-RAY DIFFRACTION31chain 'D' and (resid 35 through 45 )
32X-RAY DIFFRACTION32chain 'D' and (resid 46 through 63 )
33X-RAY DIFFRACTION33chain 'D' and (resid 64 through 76 )
34X-RAY DIFFRACTION34chain 'D' and (resid 77 through 101 )
35X-RAY DIFFRACTION35chain 'D' and (resid 102 through 110 )
36X-RAY DIFFRACTION36chain 'D' and (resid 111 through 120 )

+
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