[English] 日本語
Yorodumi
- PDB-8arb: Heterologous Complex of shortened Aeromonas hydrophila Type III s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8arb
TitleHeterologous Complex of shortened Aeromonas hydrophila Type III secretion substrate AscX with Yersinia enterocolitica chaperone YscY
Components
  • AscX
  • Chaperone protein YscY
KeywordsCHAPERONE / Type III Secretion System / T3SS / SctX / SctY
Function / homologyType III secretion system YscX / Type III secretion system chaperone, YscY / Type III secretion system YscX (type_III_YscX) / Tetratricopeptide-like helical domain superfamily / cytoplasm / PHOSPHATE ION / Chaperone protein YscY / AscX
Function and homology information
Biological speciesYersinia enterocolitica (bacteria)
Aeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsGilzer, D. / Flottmann, F. / Niemann, H.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: The type III secretion chaperone SctY may shield the hydrophobic export gate-binding C-terminus of its substrate SctX.
Authors: Gilzer, D. / Kowal, J.L. / Flottmann, F. / Niemann, H.H.
History
DepositionAug 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.accession_code

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chaperone protein YscY
B: AscX
C: Chaperone protein YscY
D: AscX
E: Chaperone protein YscY
F: AscX
G: Chaperone protein YscY
H: AscX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,36213
Polymers90,7448
Non-polymers6185
Water724
1
A: Chaperone protein YscY
B: AscX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7813
Polymers22,6862
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Chaperone protein YscY
D: AscX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0194
Polymers22,6862
Non-polymers3332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Chaperone protein YscY
F: AscX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7813
Polymers22,6862
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Chaperone protein YscY
H: AscX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7813
Polymers22,6862
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.330, 160.560, 156.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 12 through 118)
d_2ens_1(chain "C" and resid 12 through 118)
d_3ens_1chain "G"
d_1ens_2(chain "B" and (resid 51 through 62 or resid 70 through 82 or resid 84 through 119))
d_2ens_2(chain "D" and (resid 51 through 62 or resid 70 through 82 or resid 84 through 119))
d_3ens_2(chain "F" and (resid 51 through 62 or resid 70 through 82 or resid 84 through 119))
d_4ens_2(chain "H" and (resid 51 through 82 or resid 84 through 119))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRHISA3 - 109
d_21ens_1THRHISD3 - 109
d_31ens_1THRHISI1 - 107
d_11ens_2LEUPROB4 - 15
d_12ens_2LEULEUB20 - 32
d_13ens_2SERHISB34 - 69
d_21ens_2LEUPROE4 - 15
d_22ens_2LEULEUE20 - 32
d_23ens_2SERHISE34 - 69
d_31ens_2LEUPROH1 - 12
d_32ens_2LEULEUH14 - 26
d_33ens_2SERHISH28 - 63
d_41ens_2LEULEUJ3 - 27
d_42ens_2SERHISJ29 - 64

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.999943416166, -0.00731977767759, 0.0077191529029), (-0.00792649353437, -0.996621835128, 0.0817440422735), (0.00709472811581, -0.0818006026978, -0.996623462613)-0.11906853187, -51.4174248614, 76.5357825838
2given(-0.713601861862, 0.329959358311, 0.617979938679), (0.50448222249, -0.370029277578, 0.780112825768), (0.486076197667, 0.868449857849, 0.0975949510109)-36.0323695541, -49.4257240777, 55.3862720356
3given(0.99924300414, -0.0367192351853, -0.0128497643827), (-0.0366217725202, -0.999299225878, 0.00773969876367), (-0.0131249554195, -0.00726325869558, -0.999887483979)-0.45431885134, -51.4187568435, 77.7377932489
4given(-0.836896118886, 0.342203214547, 0.427202348013), (-0.332016525054, 0.303127356033, -0.893240635616), (-0.435166535116, -0.88938786026, -0.140068985636)-32.794266056, 3.21870323018, 23.1968325573
5given(-0.765313933684, 0.368166008373, 0.52796626141), (0.414332429803, -0.345927538072, 0.841821106897), (0.492567985685, 0.863010966722, 0.112200048112)-34.628368031, -51.7801877885, 55.581065039

-
Components

#1: Protein
Chaperone protein YscY / / Yop proteins translocation protein Y


Mass: 14077.914 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: yscY / Plasmid: pACYCDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0C2N2
#2: Protein
AscX


Mass: 8607.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-terminal residues GAM remain after TEV-cleavage of the N-terminal MBP-tag.
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: ascX / Plasmid: pETM-40 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q699R5
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: PO4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: reservoir solution: 0.1 M Hepes pH 7.5, 0.6-0.9 M sodium dihydrogen phosphate, 0.6-0.9 M potassium dihydrogen phosphate [1.4-1.8 M total phosphate]; protein: 10 mg/mL in 20 mM Tris pH 8, 150 ...Details: reservoir solution: 0.1 M Hepes pH 7.5, 0.6-0.9 M sodium dihydrogen phosphate, 0.6-0.9 M potassium dihydrogen phosphate [1.4-1.8 M total phosphate]; protein: 10 mg/mL in 20 mM Tris pH 8, 150 mM NaCl, 5 mM TCEP; drop size: 0.66 uL protein + 0.33 uL reservoir

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9919 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 2.63→80.28 Å / Num. obs: 34253 / % possible obs: 99.3 % / Redundancy: 24.86 % / Biso Wilson estimate: 80.05 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.229 / Net I/σ(I): 9.3
Reflection shellResolution: 2.63→2.7 Å / Redundancy: 12.93 % / Mean I/σ(I) obs: 0.61 / Num. unique obs: 2292 / CC1/2: 0.239 / Rrim(I) all: 4.831 / % possible all: 92.6

-
Processing

Software
NameVersionClassification
XDS20200131data reduction
XSCALE20220220data scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QIH
Resolution: 2.63→80.28 Å / SU ML: 0.501 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.1318
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3262 1664 4.98 %
Rwork0.2912 31730 -
obs0.293 33394 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 108.73 Å2
Refinement stepCycle: LAST / Resolution: 2.63→80.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5266 0 35 4 5305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00175388
X-RAY DIFFRACTIONf_angle_d0.35797273
X-RAY DIFFRACTIONf_chiral_restr0.0279811
X-RAY DIFFRACTIONf_plane_restr0.0028952
X-RAY DIFFRACTIONf_dihedral_angle_d9.55892032
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.731425614634
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.531239008869
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.717797549239
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS1.05995438212
ens_2d_4BX-RAY DIFFRACTIONTorsion NCS1.19195092547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.710.44121020.41452097X-RAY DIFFRACTION78.76
2.71-2.80.37971400.3612655X-RAY DIFFRACTION99.93
2.8-2.90.35681390.33622647X-RAY DIFFRACTION100
2.9-3.010.3611420.32652685X-RAY DIFFRACTION100
3.01-3.150.36911400.31112668X-RAY DIFFRACTION99.93
3.15-3.320.33191410.30112676X-RAY DIFFRACTION99.86
3.32-3.530.30371410.29312670X-RAY DIFFRACTION99.68
3.53-3.80.32391420.28962686X-RAY DIFFRACTION99.65
3.8-4.180.34441420.27992700X-RAY DIFFRACTION99.93
4.18-4.780.2691410.26052696X-RAY DIFFRACTION99.3
4.79-6.030.39621440.31092729X-RAY DIFFRACTION99.45
6.03-80.280.29661500.27582821X-RAY DIFFRACTION99.07
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)
15.414455946973.7223761437-2.815636980718.107339909930.5599276603462.62053787865-0.4468206279281.58257378562-0.61154231804-1.29432251190.251558726784-0.732546293467-0.1255077280180.4085703834930.3899765477930.267928911243-0.167173828263-0.08915410572961.008741237270.1816592570180.670080548336-12.616799681-26.353770794811.094189988
23.94888227527-0.9033170409771.251361634843.008941282281.321343217251.320094312160.2738067032010.368506757730.268789702677-0.424443435606-0.5125342338750.462103457028-0.34052641589-0.04353415345670.187624300030.272546654464-0.122165032197-0.02678063688130.7117062206810.0848113271540.83717299817-22.8803841777-18.35407955767.89136366431
38.85955492038-2.861409660772.014661891992.65991106536-3.219179102968.47542562629-0.895836547189-0.6756960831061.618808703210.6939463449571.013716463440.415077027946-0.931682847975-0.631865070633-0.0990369893240.5785318029790.128447894727-0.04730172795990.806136542262-0.07849891764580.95563476969-34.6210311722-19.65602748372.5150686471
42.84675757626-0.05557086084521.206476771076.04346700201-1.871755168723.583821171450.2010509459351.59251605436-0.666954522722-1.11872825605-0.460741290901-0.2496713956430.4825529584820.1224740189180.447932370820.350622335168-0.017714329307-0.1149671925831.55202474872-0.09918547697391.08798578684-40.6635142957-24.9828568577-1.95512699947
50.8231383917110.8777357608311.480306446652.878083256212.357001883722.983858414320.366392788772-2.33295921671-0.7206624561230.983549757553-0.3157245054541.301396632380.5999033656440.249147113089-0.1733708874220.59199658925-0.2058466628950.01312357502671.075972407270.06476440329481.07845481891-35.5141194561-29.560797416410.4644574662
60.447374224287-0.3994977441620.2636958474230.545988114509-0.3685095251440.2537953945780.2144623489640.0727380875668-0.388389548220.02072092577470.2348806795990.2386728479070.197215449016-0.04995368851460.5654476191760.350546415520.325706637246-0.23564245520.433341851603-0.2499256728921.80891870208-13.3375450563-36.428668198110.7792498477
77.316318341252.42496334834-1.293655183463.70318451166-3.421841798967.79102919037-0.140707940722-0.0617749600510.93435166332-0.336651956306-0.705836806022-0.438063843957-0.06755003187341.249261092310.7539473777310.5733316739240.0284397287629-0.03731200237630.776769073110.003914823664571.07491260365-8.38164338432-23.378949314924.3215841692
83.6611636184-1.021921615081.465201425043.341933677341.657307335523.04894329741-0.0921264373951-0.7341056837630.3741322785320.5829506546280.471576885719-0.3464919092150.4010032078510.09910136972460.2587572072330.05894758823650.08366670236480.04073944951240.8720829244690.2100097806970.636257244969-12.243974551-24.20602685367.2375840149
91.98153333995-1.669657795340.5579536498952.601909820320.5395882074282.870597216670.2675315498530.2138390798780.2680003417880.149661249275-0.2578462120020.4397329934990.373210569833-0.585298207720.03958206556280.391211317142-0.0370720270215-0.01516966404051.1598965937-0.04862374259021.00594414125-20.8059428135-30.644079730867.5001689238
105.46455521426-2.41231924654-2.642101379174.552661551032.308175997849.28187684509-0.4745701875830.09132257162450.2307216964590.2969776455920.673605043686-0.6085303174910.4147795496741.72113287209-0.1902329120680.5155657805730.110184701146-0.05027081981171.11124565575-0.09317751566441.1751722776-27.9756731968-34.311028111878.264898891
113.07634606640.4279223010182.359723505285.176604726050.9747306741693.192961811070.2189735957671.11865289961-0.7793369502270.0334170442129-0.3555894908050.8236039502640.472182811783-1.772128158760.1014548866420.43773224743-0.04722997749810.03278929510451.2317677595-0.002397612162720.933853460964-38.8217001573-29.845061726276.96313895
126.20070053453-0.4104546660824.820564838345.228193387251.328209536124.274116248220.6415532223782.447094699581.21123102597-1.52689244596-0.8670852568751.50958671788-0.422479779285-0.242425523856-0.05165507638220.5361622579160.267640698397-0.03420327169811.213117410310.002547836825471.07611333403-35.1333144847-20.636708149468.4578205641
130.4387544942950.745282288362-0.3468115843851.83923312776-1.130745715860.7778849544540.0864592355916-0.0777871922151-0.1343016142820.454801863425-0.158730387576-0.777535132795-0.1140023367660.112003153181-1.011812933550.894899332787-0.0445423938930.07842188597450.11903199117-0.0802028841421.63108010462-12.9221505363-14.104560904767.3459077072
145.08504469797-0.1413206566652.671739782162.321820925082.725280911224.79229983345-0.559678213127-0.661156287463-0.482019616993-0.663957226727-0.121251958381-0.637389261617-0.6785653625130.5936023456870.6435371643090.582564653423-0.1075658639550.09969076758371.124474121660.1585056357641.19778154241-4.68046385151-28.50777743461.1590806835
151.24950161882-0.297271433282-0.4362460884779.39545151942-6.331987994314.5427937232-0.1065392423110.748208528181-0.288487781727-0.382274552678-0.66883091787-0.06313667824950.1951552845210.1076345267710.7865302207520.42629844791-0.032922441655-0.07580584173720.7868262556280.0376803163830.808245639999-10.2459423721-26.842670184749.2127295942
160.1699456913330.4045927521260.1598660213971.41263495149-0.09940585343830.672255207241-0.215874981678-0.0381714282911-0.1940153193571.387675495260.5254731494030.317231339871-0.117057354306-0.6659924154351.359393216691.041186212680.9125986962450.1277722486661.32646049713-0.247447988130.990854140558-25.0841174121-11.540847132351.781742072
171.1461259108-0.492037721297-0.08059626291970.936835964590.6295038381830.4770059242720.2433607554960.219352974765-0.016353004622-0.1003024007850.6303343202180.3539068108960.101898808611-0.3984657044693.237148575271.517245786940.627099664076-0.2571842471650.6725059710090.4261073768270.869597802509-19.723080446-8.0904184646845.625464258
181.99092302888-0.975110811104-2.013225576115.547461635490.6929789944744.784033166520.487286306212-0.07533115331140.247537407092-0.3813406592460.730621033364-0.26939145786-0.5771010460620.4985456507991.830993577951.967180661860.220707345637-0.4374091174260.463399261663-0.2872549964550.896303154966-17.9078104426-1.8705515389350.9395117953
190.8159416425610.291726260305-0.533423910911.530999134160.9215374115071.212874262730.3391731816730.933930787586-0.09191168303260.0459377228589-0.234644517355-0.1606543287630.2157037150340.442875020940.1279610590011.90713346964-0.229905799864-0.8457929425361.802264379060.2366856984870.541686565027-10.77844624062.0903223468346.0168782564
200.1656300841190.0917787644141-0.3393043668720.8907470268780.332838962141.01250428187-0.026136798869-0.02272049758150.393761995361-0.02207819990970.1127225880530.13587393831-0.435506576569-0.1083863700460.7960423629992.807081245910.39033358881-0.02239761986520.341947112066-0.1964383882122.83331179928-11.2943277021-2.5021211714862.9893922225
216.862963878716.935084113334.583432982669.103874423051.782545381826.89999177110.671657424437-0.48417424133-2.012200916072.069059279661.071043551622.31262320447-0.509717561059-1.84092197361-1.070598372081.16228062743-0.04835860706380.1277539952031.259558058680.3931687015741.94513900575-29.0835473133-14.220851480559.7134364429
221.59310987187-0.848612001126-2.79795717991.861012981573.505034276567.80037776993-0.264620189940.3190539755390.0157658054694-0.28696001396-0.9551567573870.4999673414611.86721825194-0.9340338537230.5945776951440.7544604946280.0813811968977-0.1871588830081.27933895887-0.05504284242011.21486832066-29.4294223577-17.360767537242.8508465852
235.41077766423-1.181426036122.035932795414.66615534783-0.820645551844.91294422210.18295975809-0.9074085010660.0925810383897-0.0697006128121-0.2635956151130.555509290257-0.146592447271-1.25341515395-0.03085383339810.4799035887830.0986970338775-0.03775542007711.09060058263-0.2210043583550.818565887573-20.1191422534-26.099060223145.0348840028
242.31522512813-0.41846548097-1.950234157743.49072895361-0.08779722337294.29152946724-0.505504614183-0.379940155727-0.0619926102236-0.215082952774-0.1527730909160.5636283384160.160160616725-0.775649118430.7029890386180.789309291685-0.2400534803490.1068216325940.778357775949-0.2122743326670.941513927876-24.767026613-38.586739408728.3504618691
254.1290562715-0.296787126919-2.617739257224.231953003272.837797841948.09140998342-0.356047856947-0.625852960132-0.9614787783870.9956575075880.1736263842410.084686004951.668380842050.6965172423190.121343390970.935479296152-0.1951597410120.09294076575250.752700571697-0.03040800358160.840898851117-19.3614891805-53.716716434525.8426552113
260.5857864479521.012426548470.1166952543073.60253443444-2.043650364892.7125475077-0.3611542559530.003428222076280.446824132142-1.05852023526-0.1393076659520.125008147590.935893881797-0.619903935613-0.004660285547970.882847784073-0.2298612680950.2653866067310.599443000802-0.4887773186592.13823356206-15.2731531637-62.933362143515.0643751318
273.143143771470.2289280158882.500263556383.585570362752.946861208736.17823073134-0.108720025873-0.9423628578730.5082287215790.0240637356977-0.5504139170251.28795820208-0.39979722293-2.27228502550.4967146490290.921139805373-0.0158774516765-0.006494275531310.7534157857350.1636314847181.36541372678-24.8096580216-37.266363136725.3317157166
282.96002069916-0.379180736247-2.098498020795.45549024403-0.7090379859742.59790797590.3792825591810.7955413189490.439643514377-0.816497849615-0.306826773156-0.234596077857-0.0595816677293-0.462487113694-0.3977842853950.399991046547-0.1151153615130.004980971841071.05676793685-0.2266591875170.803747786173-20.3581743513-23.767645317932.9779063377
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 10 through 30 )AA10 - 301 - 21
22chain 'A' and (resid 31 through 81 )AA31 - 8122 - 72
33chain 'A' and (resid 82 through 101 )AA82 - 10173 - 92
44chain 'A' and (resid 102 through 121 )AA102 - 12193 - 112
55chain 'B' and (resid 48 through 60 )BB48 - 601 - 13
66chain 'B' and (resid 61 through 74 )BB61 - 7414 - 24
77chain 'B' and (resid 75 through 119 )BB75 - 11925 - 69
88chain 'C' and (resid 10 through 30 )CD10 - 301 - 21
99chain 'C' and (resid 31 through 67 )CD31 - 6722 - 58
1010chain 'C' and (resid 68 through 85 )CD68 - 8559 - 76
1111chain 'C' and (resid 86 through 119 )CD86 - 11977 - 110
1212chain 'D' and (resid 48 through 60 )DE48 - 601 - 13
1313chain 'D' and (resid 61 through 74 )DE61 - 7414 - 24
1414chain 'D' and (resid 75 through 91 )DE75 - 9125 - 41
1515chain 'D' and (resid 92 through 119 )DE92 - 11942 - 69
1616chain 'E' and (resid 11 through 33 )EG11 - 331 - 23
1717chain 'E' and (resid 34 through 47 )EG34 - 4724 - 37
1818chain 'E' and (resid 48 through 65 )EG48 - 6538 - 53
1919chain 'E' and (resid 66 through 75 )EG66 - 7554 - 63
2020chain 'F' and (resid 51 through 60 )FH51 - 601 - 10
2121chain 'F' and (resid 61 through 74 )FH61 - 7411 - 18
2222chain 'F' and (resid 75 through 91 )FH75 - 9119 - 35
2323chain 'F' and (resid 92 through 119 )FH92 - 11936 - 63
2424chain 'G' and (resid 12 through 47 )GI12 - 471 - 36
2525chain 'G' and (resid 48 through 101 )GI48 - 10137 - 90
2626chain 'G' and (resid 102 through 118 )GI102 - 11891 - 107
2727chain 'H' and (resid 49 through 91 )HJ49 - 911 - 36
2828chain 'H' and (resid 92 through 119 )HJ92 - 11937 - 64

+
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