[English] 日本語
Yorodumi
- PDB-6zg3: the structure of ECF PanT transporter in a complex with a nanobody -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zg3
Titlethe structure of ECF PanT transporter in a complex with a nanobody
Components
  • (Energy-coupling factor transporter ATP-binding protein ...) x 2
  • CA14381 nanobody
  • Conserved hypothetical membrane protein
  • Putative cobalt ABC transporter, permease protein
KeywordsTRANSPORT PROTEIN / ECF transporter / vitamin transport / pantothenate / membrane protein
Function / homology
Function and homology information


Translocases / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / membrane => GO:0016020 / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ECF transporter, substrate-specific component / ECF transporter transmembrane protein EcfT / ECF transporter, substrate-specific component / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1 / ABC/ECF transporter, transmembrane component / Cobalt transport protein / Cobalt import ATP-binding protein cbiO. / ABC transporter, CbiO/EcfA subunit / ABC transporter-like, conserved site ...ECF transporter, substrate-specific component / ECF transporter transmembrane protein EcfT / ECF transporter, substrate-specific component / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1 / ABC/ECF transporter, transmembrane component / Cobalt transport protein / Cobalt import ATP-binding protein cbiO. / ABC transporter, CbiO/EcfA subunit / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CITRIC ACID / DI(HYDROXYETHYL)ETHER / Conserved hypothetical membrane protein / Energy-coupling factor transporter transmembrane protein EcfT / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1
Similarity search - Component
Biological speciesLactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002 (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSetyawati, I. / Guskov, A. / Slotboom, D.J.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: Elife / Year: 2020
Title: In vitro reconstitution of dynamically interacting integral membrane subunits of energy-coupling factor transporters.
Authors: Setyawati, I. / Stanek, W.K. / Majsnerowska, M. / Swier, L.J.Y.M. / Pardon, E. / Steyaert, J. / Guskov, A. / Slotboom, D.J.
History
DepositionJun 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Energy-coupling factor transporter ATP-binding protein EcfA1
B: Energy-coupling factor transporter ATP-binding protein EcfA2
C: Conserved hypothetical membrane protein
D: Putative cobalt ABC transporter, permease protein
E: CA14381 nanobody
F: Energy-coupling factor transporter ATP-binding protein EcfA1
G: Energy-coupling factor transporter ATP-binding protein EcfA2
H: Conserved hypothetical membrane protein
I: Putative cobalt ABC transporter, permease protein
J: CA14381 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,25329
Polymers266,23310
Non-polymers5,02019
Water00
1
A: Energy-coupling factor transporter ATP-binding protein EcfA1
E: CA14381 nanobody
G: Energy-coupling factor transporter ATP-binding protein EcfA2
H: Conserved hypothetical membrane protein
I: Putative cobalt ABC transporter, permease protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,67013
Polymers133,1175
Non-polymers2,5538
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18190 Å2
ΔGint-87 kcal/mol
Surface area50360 Å2
MethodPISA
2
B: Energy-coupling factor transporter ATP-binding protein EcfA2
C: Conserved hypothetical membrane protein
D: Putative cobalt ABC transporter, permease protein
F: Energy-coupling factor transporter ATP-binding protein EcfA1
J: CA14381 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,58416
Polymers133,1175
Non-polymers2,46711
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17550 Å2
ΔGint-91 kcal/mol
Surface area49790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.290, 110.470, 110.500
Angle α, β, γ (deg.)88.997, 102.271, 102.244
Int Tables number1
Space group name H-MP1
Space group name HallP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 2 through 280)
d_2ens_1chain "F"
d_1ens_2chain "B"
d_2ens_2(chain "G" and resid 2 through 283)
d_1ens_3(chain "C" and resid 1 through 501)
d_2ens_3(chain "H" and (resid 1 through 207 or (resid 601...
d_1ens_4(chain "D" and (resid 6 through 53 or resid 55 through 301))
d_2ens_4(chain "I" and (resid 6 through 53 or resid 55 through 301))
d_1ens_5(chain "E" and resid 2 through 126)
d_2ens_5chain "J"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERSERA2 - 280
d_21ens_1SERSERJ1 - 279
d_11ens_2ALAGLYB1 - 282
d_21ens_2ALAGLYK2 - 283
d_11ens_3METARGC1 - 207
d_12ens_3LMTLMTD
d_21ens_3METARGL1 - 207
d_22ens_3LMTLMTM
d_11ens_4ILEALAG1 - 48
d_12ens_4VALHISG51 - 261
d_13ens_4LMTLMTH
d_21ens_4ILEALAQ1 - 48
d_22ens_4VALHISQ50 - 260
d_23ens_4LMTLMTR
d_11ens_5VALSERI2 - 126
d_21ens_5VALSERS1 - 125

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5

-
Components

-
Energy-coupling factor transporter ATP-binding protein ... , 2 types, 4 molecules AFBG

#1: Protein Energy-coupling factor transporter ATP-binding protein EcfA1 / ECF transporter A component EcfA1


Mass: 33166.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: His-tag with TEV cleavage site an N-terminus
Source: (gene. exp.) Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002 (bacteria)
Gene: ecfA1, cbiO1, Ldb0424 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1GBJ0, Translocases
#2: Protein Energy-coupling factor transporter ATP-binding protein EcfA2 / ECF transporter A component EcfA2


Mass: 31672.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002 (bacteria)
Gene: ecfA2, cbiO2, Ldb0425 / Production host: Escherichia coli (E. coli)
References: UniProt: Q1GBI9, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances

-
Protein , 2 types, 4 molecules CHDI

#3: Protein Conserved hypothetical membrane protein


Mass: 23008.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: StrepII tag at C-terminus
Source: (gene. exp.) Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002 (bacteria)
Gene: Ldb0463 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1GBG0
#4: Protein Putative cobalt ABC transporter, permease protein


Mass: 30290.283 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002 (bacteria)
Gene: cbiQ, Ldb0426 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1GBI8

-
Antibody / Sugars , 2 types, 9 molecules EJ

#5: Antibody CA14381 nanobody


Mass: 14979.450 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lama glama (llama)
#7: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 2 types, 12 molecules

#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 71.11 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 70mM citrate, 22% PEG 300

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.8→48.83 Å / Num. obs: 104704 / % possible obs: 96.7 % / Redundancy: 1.72 % / Biso Wilson estimate: 85.15 Å2 / CC1/2: 0.997 / Net I/σ(I): 4.7
Reflection shellResolution: 2.8→2.87 Å / Num. unique obs: 7625 / CC1/2: 0.195 / % possible all: 95

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JSZ

5jsz


Resolution: 2.8→48.83 Å / SU ML: 0.7043 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 38.0686
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2764 5211 5 %
Rwork0.2423 99073 -
obs0.244 104284 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 110.3 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17885 0 338 0 18223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118606
X-RAY DIFFRACTIONf_angle_d1.285825218
X-RAY DIFFRACTIONf_chiral_restr0.06452953
X-RAY DIFFRACTIONf_plane_restr0.00833135
X-RAY DIFFRACTIONf_dihedral_angle_d19.45356778
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.741179805629
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.682950415462
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS1.2684072142
ens_4d_2GX-RAY DIFFRACTIONTorsion NCS3.56149900773
ens_5d_2IX-RAY DIFFRACTIONTorsion NCS0.89093080817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.830.50011740.4623327X-RAY DIFFRACTION95.53
6.9-8.680.20131710.18983249X-RAY DIFFRACTION95.24
8.69-48.830.23771660.22163180X-RAY DIFFRACTION93.05
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)
13.044623695-1.935317324732.208448211133.14222730728-0.7785218684575.08044512864-0.7815936430060.9320749413450.2279399546040.2680883274-0.1691480627220.214083705784-0.7866571716421.538669750220.1521311694810.630045452447-0.112034558988-0.04563822879081.22959717450.3798276545450.5472183883940.90553981706879.269496057191.7740762564
21.63522688328-1.245503181480.6412171938594.06298626952-1.413071239813.1023464293-0.091535438036-0.0516674334445-0.114042079937-0.224587487290.1219692272550.02632269193770.175555829421-0.22180694660.08273707734210.550900493088-0.155287716068-0.04946672174440.6590156725340.06828345739290.69784264314-9.6102630135695.605417010685.5494371395
33.38325464404-1.333716559750.1347991790064.31306928357-2.660887718954.08954896278-0.132264023624-0.2253958113920.07911794599940.316072777116-0.181033861724-0.1729768151460.185691103450.2306662909230.3122776782210.63534291802-0.0982335428828-0.005000963685620.5901533118540.03390687492920.560030153076-10.372234273481.603146706199.33816493
46.07339739364-1.619428003430.7839720178438.942062515750.03757195985919.22412945267-0.8144417386570.525242478834-0.9644563440960.7358930782880.1087204705990.1307969749120.02071228537490.3850678966640.5648098090031.19363324284-0.2012485740940.1406969729121.122324485130.3623083113091.28430033141-19.962293379270.272565951115.030823295
57.370263212491.15590118366-0.3159913490965.2385308005-1.557632401646.24918223712-1.44803952251-0.1282429613511.302900818460.6917848028490.374232336726-0.135173102178-1.49974712935-0.172389124041.103712877421.28527586529-0.0663113998413-0.5162586885271.000552537110.1352041461511.29741291041-39.225865878159.599774215260.5101745693
68.94623095326-0.215902246352-4.26200433556.95475246514-0.6007883838773.02971336421-0.760142550119-0.196817466007-1.4152293298-0.633964138822-0.004773839473950.959708994931.92367799928-0.1243213666381.038378596330.97662430207-0.05624666773530.02011777554480.6430855881270.1008720822561.23849821838-41.568274572251.166919176471.2743802867
78.21508681831-1.09051874486-0.8160808953155.52046467806-4.620011705396.035425988090.0929538649174-0.4449588530690.6741759211960.395347511390.02126408122790.414896964651-1.961233968240.880125410252-0.1992091373630.742720423251-0.0848630984851-0.02377491498550.665539079654-0.008812848274010.785366376894-43.887553251959.658385321365.1992636143
88.22337585077-2.979063500135.680460616673.98890526578-2.221244247394.06260197549-0.7270492167210.626749283283-0.5749746541280.4163910680560.387458631851-0.707623825747-0.8753570550380.388181910724-0.416372358891.6688645564-0.0963359922850.01543946152180.6250614025540.01372915281511.07018936119-49.703776787549.740182983357.3806277325
94.77236146285-3.1530449491-1.150088332665.24297429333-2.423142690535.69606729789-0.130897346342-0.333120142636-0.9383882597040.180098360947-0.2746438417550.4039849255720.1309723192440.2538001996970.05746829196390.761173774298-0.203262803032-0.03314729941690.7754245570460.2445571873620.874322993943-59.821178781261.649606826168.7623425835
103.48104116894-0.759072755595-1.564786339123.589673839840.08542047463676.50647741788-0.3793506160430.0187239304181-0.762573637334-1.622517213121.486777640752.316909610790.545991414653-1.10012901951-0.986702802261.50266726696-0.505980405329-0.2361969910031.401072070960.4915417903191.65497721868-70.498651256557.561608468873.3382637341
112.94339867226-3.672092976951.418437534664.31532409746-2.069834156284.34690698521-0.258338507695-0.62681112102-0.5489173556260.17107790030.299581886836-0.09157539774610.28420975939-0.106639665476-0.1805847461110.870925117542-0.2786042979040.05774620980640.7856150757730.1345720525651.06539958241-62.276246200864.248623640679.3572077602
123.534567527483.561024771360.8276218315066.007010161515.293942039518.4564648138-0.251699772833-0.883520218968-1.176405953710.746178043271-0.645155659603-0.5364526312440.7776622419520.2731123522510.9471259868361.66080628794-0.410113773287-0.431738516830.7704035721250.1685327167641.85030806426-54.832145110356.81201964386.0962898209
136.95967720465-1.148819722262.881547244540.3104525323690.4093323543855.34396397975-0.05334869249650.379071929111-0.237255481812-0.2326006079570.1164825031590.3544503934120.08031612217320.806580534834-0.09796406682580.92793587437-0.0834719410591-0.01645763265360.5599049581690.03266002229671.07733433902-36.750270803656.236300466780.1493303921
147.197740643226.39906869676-1.030724950898.185356558510.1888423184352.234319892480.1061346833990.6745899404711.467194302361.31604760542-0.455692930548-0.199292126902-0.3890378248691.09644283626-0.2241362543371.07452374070.132057590877-0.1958404673861.013322677480.2743117976641.42982250749-32.834825584854.789774924299.3432385551
152.298175014231.204605399042.604593151821.44417179231.054926398149.48510230317-0.0532131664618-0.7811122668410.164129802115-0.497216993333-1.037257063770.940192667145-1.44943174703-2.72244949510.9200444021760.694931574908-0.0654167170947-0.02589059150331.30811321074-0.02460909722541.09180824884-60.269398157992.133380189270.2635969596
163.09655580365.172148340183.322294118338.987758361855.032828730384.276677591571.68067750020.3803527538390.3509857787130.54991992785-2.01456577953-1.514899919930.285664697103-0.7909134928150.05028097861870.8418435785630.2623804340480.1589560531751.992634848390.02768224850841.29096831411-62.076825384475.242725275749.1013252065
175.439242049612.611391221873.004375538633.25219266612.48876758412.210514578970.6863181733782.89428797945-0.325586197117-0.597791607093-0.345685027888-0.3879376590783.649424546281.045902968290.1950363619961.89272379023-0.190313590811-0.4115557480411.659109810590.1248317486371.10483068662-65.481407719178.709443155645.5753147597
186.012456480342.00350112570.125768900837.40361467218-1.897748824963.95324251049-0.0816257087843-0.05981420235350.2412451728650.543779297322-0.971199364375-0.00707353248065-0.181516387827-0.5609254842171.108763874770.633735277324-0.221008163097-0.1852875899370.9463139576170.1458456723110.730263298346-64.3420433691.135126545756.5183589696
196.690270111352.84313682467-1.329169986414.251772019173.556036565825.843519165440.330547552058-0.8377682216490.4917858544420.427360177307-0.381244605669-1.59946115635-0.669902983907-0.370661584981-0.08159008518370.916897267484-0.172250725-0.1174211912270.9834138245430.2694586766430.793669343531-60.985817114588.401682003339.9912061304
206.863431978524.05547856708-2.804078101056.773271719450.4449294860285.935501255440.0223624116972-0.0569809622857-0.1006538511970.932021784916-0.996898462180.930579806970.37456991922-1.163702042230.05634274614420.898695294919-0.135546751319-0.01919294878320.654882181866-0.04102420302890.875379289168-76.155850917290.834618144961.5642585957
211.99178750726-0.7008933477160.7678830538394.98435134552-2.418222820481.30817318369-0.1549363335471.14917776676-0.216539188196-0.700274306122-1.15261046719-0.49046477033-0.07318201430510.878579588511.759232631080.801763162046-0.158132282774-0.2543484530731.272829350380.2412919292390.752573291224-72.488930976491.034292758342.6400628961
222.498594316381.356125057881.443301421644.95959335281-2.765813027385.138868452750.2809606328-0.1142721192820.571650807064-1.017061408220.1762457200310.8271528729740.3892544596270.0395767162567-0.368305651390.5163347502080.01785179160780.07792538460780.6127674746830.02684473296270.692639355146-71.996328493682.063005565654.6846914816
237.316452105521.13291912393-0.3561441796939.167836323142.251342998716.54287517387-1.481712989012.468033766021.11843692651.957792554231.64855781628-0.9736639030430.2833483380970.869266313449-0.7704431798741.54641921288-0.00176462958761-0.4813440933961.36881467930.2429623284321.25461097157-33.410059630693.557081673652.5920999246
242.578665397151.842557074181.050329583413.994907089952.734531798812.829818141890.001395680560030.673824958026-0.3270809005320.795962104473-0.399474493612-0.787826012749-0.5504769430341.32794671310.1767089298230.806340703541-0.143776898167-0.2889823160761.146426899810.09286041507970.65221630932-44.100885801191.98716991237.2939998056
253.126921064972.683446744571.354081233483.334224294541.870864466161.07119435281-0.286074042231-0.4900567502621.23548267605-0.378005150630.8503938521991.069173198941.07091438125-0.605481274052-1.045522652481.62540348181-0.194663580937-0.4801500201880.8817356434730.1629896986161.93023938974-60.717064236880.856808481617.1987042346
266.940844070450.681206841027-6.042855494272.256670101-2.311629768246.61240260074-1.24580586056-1.71255770070.470902868295-1.86718001353-0.386958933311.31731655649-0.4959845563020.926535035117-0.8175262394221.761374300130.372968022362-0.5453108075872.88009949939-0.8970127363621.5246728563-50.938294046386.373500389414.2235749597
271.39979089126-0.84794990556-2.13271316740.3539207138590.3977653342732.731639850760.1802774655341.15018421359-0.067632145538-0.00657895520071-0.3244967937910.325592649356-0.94238704297-0.01631885182660.2790625811880.81867458066-0.215035085998-0.1395603274621.290473240870.08465818875640.745371730249-50.43403894390.86657865655.2080749381
286.01251990496-4.099528140382.341412271943.0913534953-2.593819520464.444536399780.3154311640671.37805493172-0.5455965618710.158887405661-0.5033371691270.3546601758610.244010544165-0.802812405984-0.3941076870440.971127977687-0.1957800596510.3281449851640.997299089978-0.2285887234561.61538382344-66.228221630564.644133201655.4098036089
291.48831113648-0.252910891814-0.1030193321660.114700121897-1.224529477043.53083062193-0.1967587157040.364592773647-0.0422232970225-0.283852884046-0.1814663695-0.0449108433429-0.7633063916830.2559825648520.2867434154610.931664506976-0.130217162472-0.1949829508840.9085780965170.1834300431750.930563895525-49.341799980396.42403085559.4501519472
306.09553415011-5.31064540057-0.6827016774949.43242834207-2.906449356032.610489291570.6605045430350.312263377697-0.365171244105-1.20396912294-1.09335804040.374403361905-0.344021303432-1.238038917410.3462314301110.6474037957410.007011712818790.04876906469161.00552969111-0.01871545225150.696152808451-24.843823158980.841928893756.5017310347
312.223871942812.297806453312.475631827453.855249847674.085341442444.27829117412-0.2573212318280.6756511433090.732779352198-1.33431437599-0.2970411441380.313018382202-0.648365249634-0.3815064510210.08070583479820.818332069004-0.0522240703050.1973623064011.00443698121-0.05103108901170.500965994256-19.918422412491.24302441259.9851137225
323.81197059973.086149628570.705906987012.828772174720.5587613412080.215878284173-0.2111001868071.33605418428-0.20883969476-0.08141520286780.4146998200431.17454074453-0.752650766461-0.407733555010.1895147719380.5843403069180.0631517106550.1291813289150.421792209207-0.1878741694910.621284659876-21.461836978181.124460440666.0415889859
336.64788481965.260925937562.583662211024.237251758611.981680047841.035744807170.997966386899-0.656419186093-1.281422698220.0161427340613-0.645267019565-0.6255967205560.2149808204530.2844420499420.3307623973650.7197894361570.1464537773440.1172934681060.582009643871-0.3840812408110.613086109008-17.000944379880.588430327667.8638937369
345.62085482655-1.065555711410.3858956085947.66029605648-0.5512018585435.065930876090.1582974703451.14060032112-0.0376922816755-0.463769238323-0.125083995009-0.0689644905607-0.5897965328590.483362363507-0.1018203863050.681945846514-0.182737669774-0.02061224834380.895392122882-0.05509229733730.561145201627-14.320063605882.075962305859.3210043279
354.125076736721.816560483191.61757234318.140826843476.498175290945.17757777468-0.235627499078-0.977958359043-1.224177265150.835103313389-0.3733934688710.672888480590.5565705117680.04914277365640.4814105464370.727747910902-0.03584830297850.1469608606370.470162246859-0.01445564741920.91077818716-22.371808199375.147330891761.689186841
367.623754079385.104904891460.6866748618723.810517113510.7699027598130.4123700901870.728005069175-0.910742433896-1.267837746280.577785436733-0.82138011973-0.7307273758350.4187161580530.6355372317260.2233117264960.5367617562880.0065140278129-0.1281361323550.525248447464-0.03893631976210.740194812696-12.704387203889.405674395572.7330913037
374.236819975130.6988330527292.223262249653.97130891913.849847910914.19286398256-0.06325224288080.288289711438-0.117562164082-0.284424618864-0.456202301484-0.0402452738233-0.034325352395-0.7631842278661.010600266750.798278773104-0.1327162987840.04649052826950.9685533717690.0303466246340.617584047164-26.183265461781.279200314964.5969419997
383.542163115915.435214823462.668683328399.297522494132.057825482178.37366566273-0.3921450464710.1662938354661.11200484603-0.7410971253130.7052033627422.690570193490.556321144959-1.19342149507-0.05578685529950.856357775625-0.186352370667-0.04718696521360.9672189476130.4167151422721.35353889103-61.486548328988.661981200798.0123297265
397.146941721370.504577297658-1.078077120965.78970887428-1.41800405771.71693741022-0.828963817149-1.4165141993-0.1065392947250.8637139226410.3351028735490.7561697803640.146192683602-0.3232058926330.1654234732230.5706233913310.1247072923750.2314882779220.6110569608890.4026664312320.974153379301-53.140014987883.744463744799.5840051651
402.593837191251.11407229196-0.1772835914654.26919103604-1.913542462272.37942281897-0.254381490036-0.03504084553360.209934213178-0.1348381856430.479433077070.282423287584-0.2841771076520.0327426843977-0.1507136643710.582501065535-0.06180158457-0.02430923837270.6858606665840.113884042990.641619408091-52.191811690794.470221518486.6085501588
413.768346740730.754959935224-1.003706017922.040934950630.4939429139893.23894301703-0.3775784034220.146647897478-0.176462953327-0.437994214430.1912523268820.01894560291290.3763999720460.3328460643660.177106750360.590830784802-0.06205019914580.02018863758680.7980343049240.1444790620240.649418220155-35.430049274290.98259277274.0998109569
423.43524515932-0.596285321345-0.2150706340052.20881795787-1.683558283145.04272512233-0.524001696788-0.199878341557-0.4129927151380.2295209046620.3323684828790.3673344178790.401531440715-0.4037274193470.005300088120080.83163224186-0.0562407080061-0.019314070.7854419112410.2292890135070.903415895754-45.017287164479.689390921894.2628474638
436.70224481353-1.744550579020.5650220457292.21615354661.545163997644.07782695219-0.5901034818060.07517034209250.482717235383-0.0735088620988-0.0096286057542-0.5509188660541.142259270810.9056609516990.9455385805221.18585857060.3879892190790.1096681444471.14814368690.453445634081.30385962528-36.153363802962.5065947415107.144565784
441.88600006272-2.52318068631-0.969086617475.15588216344-2.221974542547.50730663251-1.20813865570.888649265840.4420304165021.482374478620.682476804298-1.18945038788-0.3169608279211.20275493774-0.05884550464682.05066198561-0.833196530047-0.4792665131461.430914725480.3206460229480.98628803419-15.3679456311116.559148973123.763894882
456.53696472757-1.973162146232.067878438644.560343032511.13308842771.82840868135-1.819718909230.7178824424770.99721786863-0.5024664463920.8576957812380.489623200733-2.076975964951.066698264490.3153839100131.62274704365-0.283366130388-0.2231613813511.187811801240.05287491932520.611925714992-15.589462665107.857084663123.662283313
463.21926610948-3.08526969751-2.218655649483.897294275581.384677585761.402348467460.158598128796-0.7031304260050.03454378078110.4886504139310.010346433803-0.5176237810150.3004195758590.198560265039-0.1909841841890.988828888745-0.112281265734-0.295266264570.9452782154380.1610358356960.6815318493642.06304358326109.856910789120.920889878
472.72245721147-0.58039368376-2.558189235365.96381404796-2.385938957323.61095036348-0.0500750070153-0.469888687277-0.408297762438-0.305286712635-0.01936264783160.01717425895240.6736607960570.00372892106828-0.06587052132250.7780512431040.0578997378423-0.2423615883611.04630805620.158012353410.7311005314866.3054550503998.0481840762114.275387279
482.300235055160.8771426744152.720143696033.351497108421.835686155744.84604725385-1.23027526343-0.839799300519-0.597553943879-0.468769653710.6459358410680.3768734535110.944091002920.416693598682-1.947693298991.5092317541-0.835513191688-0.5178553663952.903050824580.4347114230790.709075449895-1.2966601750490.951479581120.941436592
498.40691017579-0.032112792806-1.848657387714.769424615170.9050440886550.5724633498180.538321875170.6960025177320.210885566638-0.130768220909-0.1192599960820.472947168357-0.469411579074-0.397559037282-0.5768436319261.107645537830.0915600603284-0.009383447953171.694327313540.1823040968450.5953154867-15.980169061697.7974984004123.705299136
505.3213806889-1.748736402140.2314055149446.142608072150.1918704370294.692130226660.5129542616940.6323249161420.955991275552-0.197833213675-0.7380040428710.224348709338-0.7732413627980.2300779455860.201548061020.921900675689-0.1771418185940.1688583294811.133898412120.07412045797070.779181613129-24.719968142183.0313800053121.405729722
512.43332351168-2.30888895124-1.16469978335.287351079856.016727373257.71537263190.5057169466290.128555162799-0.915206004408-1.214357139270.859124902747-2.52410033513-0.8888722866160.978221650044-0.1832542159040.418041373723-0.1295437110870.0497162790541.02550083058-0.1474611316911.129665500534.46426522641107.97220702886.6534998379
527.928998394980.6849929383272.509816263740.1335730894-0.3973071686355.81169074051.24507891482-0.8307899281410.5493217285490.208002642440.7908085349491.60257565778-1.04474567793-2.30667696836-1.710680394630.850112690730.04773044332250.3985202745011.668255805040.2564537818841.911012196346.03801981534128.677595826104.240419094
537.9423130364-0.4579384963762.421891213844.737162247924.232405928854.802570542380.153203506562-0.9477175228191.908514365190.3071232061590.09314800907480.4691256016571.18466731336-1.141976001740.1750373346591.86300607773-0.491408361589-0.2225627666541.125644175680.1767213674041.230109369999.23994467465132.154378333100.920847247
543.801435103362.008248738530.3995046746793.34374100560.1028616532614.07959040576-0.04751716749930.7351643662060.328684148032-0.6909582540920.415652120074-0.187324214133-0.0379617480784-0.142298118443-0.6094476757220.913727871173-0.211792465528-0.1514545602620.7831686985310.2580758894631.0050808819710.5723459617124.61608919887.5475880874
554.61893599961-2.45155967735-0.8015046219345.50416679749-4.03432997167.70082248090.33619311878-1.26234065168-0.9340203597910.5274474503740.147704923677-0.859980715859-1.058133066840.4362674994481.090266936761.982991820020.255506835654-0.7962045411911.032788594370.06939753796761.3715532232927.7205278557105.2813903595.4293953224
561.851792856171.11265948177-1.399868103844.935767856221.657057398622.43437000510.278179093106-0.1915646762112.059318467770.1933724402510.6739012629260.0377434569246-0.325024770033-0.1329738194650.6906183272050.791865248858-0.257450457802-0.1395366935110.7551757878540.5488047333712.3723048519416.4596099954134.76007468888.4967580458
572.58770460903-0.3154523947830.6582453052841.7287550388-0.9531880412922.414606313130.2012212584390.03149488366190.317197401110.243282911917-0.636161422684-0.986282983251-1.085112149750.729172679065-0.1051576177390.7033168169040.01311481976520.1063567501910.74694791738-0.01954802449450.39830499971415.8764060425124.49489584696.872002463
588.79014335636-1.4178310349-5.434452149043.39497009275-2.504013426947.32750855682-1.120471300680.7680643768390.5844831632910.326283621283-0.02893583249650.6428254072061.5373069361-0.9290139157240.7618474884271.49233557658-0.508356885186-0.1803676786941.00325168280.139229357631.31102396964-21.2477551234124.91514138386.4540258146
592.640905542130.4865705702312.280201989255.07102453272.144421425885.454230004630.190939372276-0.4773786727970.7631927320790.09458524175920.2378397139171.375081016790.822052773867-1.19471745911-0.2818700008330.76554143541-0.2992755381420.02064011643620.784384991276-0.1214932360841.01287208354-11.7675992313141.10113678387.7478048428
601.142524939312.111026547870.1878823481184.171957841691.461958085333.99759029172-0.477774447449-0.2952896007781.634507847221.06047870121-0.3521180808721.95324495532-3.983137245180.7545784138870.5978067179481.99401919475-0.3129587867380.02775800730091.4033343249-0.2205514232851.28916761063-0.441772845545163.16391757696.7738823795
612.66436830262-0.0945208337145-1.54150173211.41011954723-0.3884051300790.09413722352120.0109257831964-0.2319630071830.7479468429540.118818886566-0.296070108337-0.147260855129-0.3358241907660.3964713660390.2982556053340.721319523879-0.221257369656-0.1846737235160.7562535897390.01442109240810.846764570087-1.66161980861120.20078570693.1575795166
621.42957005707-3.29836818796-0.2985773705087.201725974750.2970251144042.137452337670.3964514372671.558516546881.51233389488-1.26049391101-0.485232678044-0.672866463266-0.7970768061760.2782274707480.2445595438841.14289276315-0.208214489525-0.1594263112081.2723727630.6319198378621.38755853488-12.2087761242110.74333830874.8522682044
636.17424117688-0.1815273837160.01640946512710.183137287042-0.600764975983.677043977710.00234334135096-0.5625895493571.44357568465-0.637484926358-0.4270012972050.3314654532870.988094646207-0.4123993731390.0613157271371.14536457057-0.300529849078-0.2796342129670.564177741080.1695972090960.823789365282-14.7818620629142.67930199372.7442676764
644.657585537680.2048144437960.03748029780184.0038991610.9645878218462.745205917930.441041312309-0.6318677483090.534581712967-0.3446654046830.84257420026-0.540641231678-0.4093898157781.77995512206-0.3910164257350.6219552088750.0615060708257-0.08914376861010.583878303209-0.03986122309881.0526797703-31.0936873738122.57473382199.8218245941
654.053388312831.147736444071.118894613531.463707931911.527160543122.49238490189-0.509909827090.3300520164711.62906914408-0.5200601434610.408498324522-0.00718826470678-1.296848294451.0466232855-0.01724107518560.871797002093-0.0296091653032-0.02905418014770.524083793968-0.07280327409390.99218424464-35.5737975682116.0494032191.1224580706
664.763057389251.491405031752.121540879773.957377973993.138945588383.86485571666-0.315223374202-0.007228519722850.461374102296-0.230163011760.2453058263890.205490521725-0.3277845226530.3165748728640.008070726944050.659398346654-0.0103727474225-0.04083620322490.586064442127-0.03902788360470.826588121789-38.6969588238115.10520475999.175395152
674.437665521950.8432994442760.1263343566965.174458252081.917757636721.48654873627-0.18846372746-0.00558443427793-0.007350148017210.164110321680.602401828281-0.4280574600420.441937085538-0.41507345953-0.04171037110140.689207240604-0.02265964111-0.08226105241790.7014300882960.1137634947710.744752734795-35.2861301533110.13631618794.3140350142
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 45 )AA1 - 451 - 45
22chain 'A' and (resid 46 through 160 )AA46 - 16046 - 160
33chain 'A' and (resid 161 through 245 )AA161 - 245161 - 245
44chain 'A' and (resid 246 through 280 )AA246 - 280246 - 280
55chain 'B' and (resid 2 through 21 )BB2 - 211 - 20
66chain 'B' and (resid 22 through 39 )BB22 - 3921 - 38
77chain 'B' and (resid 40 through 62 )BB40 - 6239 - 61
88chain 'B' and (resid 63 through 78 )BB63 - 7862 - 77
99chain 'B' and (resid 79 through 102 )BB79 - 10278 - 101
1010chain 'B' and (resid 103 through 132 )BB103 - 132102 - 131
1111chain 'B' and (resid 133 through 177 )BB133 - 177132 - 176
1212chain 'B' and (resid 178 through 194 )BB178 - 194177 - 193
1313chain 'B' and (resid 195 through 247 )BB195 - 247194 - 246
1414chain 'B' and (resid 248 through 283 )BB248 - 283247 - 282
1515chain 'C' and (resid 1 through 28 )CC1 - 281 - 28
1616chain 'C' and (resid 29 through 38 )CC29 - 3829 - 38
1717chain 'C' and (resid 39 through 46 )CC39 - 4639 - 46
1818chain 'C' and (resid 47 through 80 )CC47 - 8047 - 80
1919chain 'C' and (resid 81 through 93 )CC81 - 9381 - 93
2020chain 'C' and (resid 94 through 124 )CC94 - 12494 - 124
2121chain 'C' and (resid 125 through 165 )CC125 - 165125 - 165
2222chain 'C' and (resid 166 through 207 )CC166 - 207166 - 207
2323chain 'D' and (resid 8 through 20 )DG8 - 203 - 15
2424chain 'D' and (resid 21 through 84 )DG21 - 8416 - 80
2525chain 'D' and (resid 85 through 94 )DG85 - 9481 - 90
2626chain 'D' and (resid 95 through 107 )DG95 - 10791 - 103
2727chain 'D' and (resid 108 through 183 )DG108 - 183104 - 179
2828chain 'D' and (resid 184 through 197 )DG184 - 197180 - 193
2929chain 'D' and (resid 198 through 264 )DG198 - 264194 - 260
3030chain 'E' and (resid 1 through 17 )EI1 - 171 - 17
3131chain 'E' and (resid 18 through 32 )EI18 - 3218 - 32
3232chain 'E' and (resid 33 through 39 )EI33 - 3933 - 39
3333chain 'E' and (resid 40 through 60 )EI40 - 6040 - 60
3434chain 'E' and (resid 61 through 83 )EI61 - 8361 - 83
3535chain 'E' and (resid 84 through 99 )EI84 - 9984 - 99
3636chain 'E' and (resid 100 through 109 )EI100 - 109100 - 109
3737chain 'E' and (resid 110 through 126 )EI110 - 126110 - 126
3838chain 'F' and (resid 2 through 21 )FJ2 - 211 - 20
3939chain 'F' and (resid 22 through 45 )FJ22 - 4521 - 44
4040chain 'F' and (resid 46 through 116 )FJ46 - 11645 - 115
4141chain 'F' and (resid 117 through 147 )FJ117 - 147116 - 146
4242chain 'F' and (resid 148 through 245 )FJ148 - 245147 - 244
4343chain 'F' and (resid 246 through 280 )FJ246 - 280245 - 279
4444chain 'G' and (resid 1 through 16 )GK1 - 161 - 16
4545chain 'G' and (resid 17 through 39 )GK17 - 3917 - 39
4646chain 'G' and (resid 40 through 131 )GK40 - 13140 - 131
4747chain 'G' and (resid 132 through 177 )GK132 - 177132 - 177
4848chain 'G' and (resid 178 through 193 )GK178 - 193178 - 193
4949chain 'G' and (resid 194 through 234 )GK194 - 234194 - 234
5050chain 'G' and (resid 235 through 282 )GK235 - 282235 - 282
5151chain 'H' and (resid 1 through 28 )HL1 - 281 - 28
5252chain 'H' and (resid 29 through 38 )HL29 - 3829 - 38
5353chain 'H' and (resid 39 through 46 )HL39 - 4639 - 46
5454chain 'H' and (resid 47 through 117 )HL47 - 11747 - 117
5555chain 'H' and (resid 118 through 124 )HL118 - 124118 - 124
5656chain 'H' and (resid 125 through 163 )HL125 - 163125 - 163
5757chain 'H' and (resid 164 through 207 )HL164 - 207164 - 207
5858chain 'I' and (resid 6 through 20 )IQ6 - 201 - 15
5959chain 'I' and (resid 21 through 84 )IQ21 - 8416 - 79
6060chain 'I' and (resid 85 through 104 )IQ85 - 10480 - 99
6161chain 'I' and (resid 105 through 224 )IQ105 - 224100 - 219
6262chain 'I' and (resid 225 through 244 )IQ225 - 244220 - 239
6363chain 'I' and (resid 245 through 264 )IQ245 - 264240 - 259
6464chain 'J' and (resid 2 through 17 )JS2 - 171 - 16
6565chain 'J' and (resid 18 through 39 )JS18 - 3917 - 38
6666chain 'J' and (resid 40 through 99 )JS40 - 9939 - 98
6767chain 'J' and (resid 100 through 126 )JS100 - 12699 - 125

+
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://pdbjlvh1.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