[English] 日本語
Yorodumi
- PDB-8zys: Crystal structure of HSF5 DNA-binding domain in complex with 3-si... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zys
TitleCrystal structure of HSF5 DNA-binding domain in complex with 3-site HSE DNA (25 bp)
Components
  • (DNA (25-MER)) x 2
  • Heat shock factor protein 5
KeywordsDNA BINDING PROTEIN/DNA / HSF5 / HSE / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


male meiotic nuclear division / XY body / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / sequence-specific double-stranded DNA binding / spermatogenesis / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Heat shock factor (HSF)-type, DNA-binding / HSF-type DNA-binding / heat shock factor / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Heat shock factor protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShi, X. / Zhang, Q. / Liu, W.
Funding support China, 4items
OrganizationGrant numberCountry
Other government2021XZL06 China
Other governmentCSTB2022TIAD-STX0015 China
Other governmentZXZYTSYS02 China
Other government23JSZ01 China
CitationJournal: to be published
Title: Crystal structure of HSF5 DNA-binding domain in complex with 3-site HSE DNA (25 bp)
Authors: Shi, X. / Zhang, Q. / Liu, W.
History
DepositionJun 18, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heat shock factor protein 5
B: Heat shock factor protein 5
C: Heat shock factor protein 5
D: Heat shock factor protein 5
E: Heat shock factor protein 5
F: Heat shock factor protein 5
G: DNA (25-MER)
H: DNA (25-MER)
I: DNA (25-MER)
J: DNA (25-MER)


Theoretical massNumber of molelcules
Total (without water)116,50310
Polymers116,50310
Non-polymers00
Water6,539363
1
A: Heat shock factor protein 5
B: Heat shock factor protein 5
C: Heat shock factor protein 5
G: DNA (25-MER)
H: DNA (25-MER)


Theoretical massNumber of molelcules
Total (without water)58,2525
Polymers58,2525
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Heat shock factor protein 5
E: Heat shock factor protein 5
F: Heat shock factor protein 5
I: DNA (25-MER)
J: DNA (25-MER)


Theoretical massNumber of molelcules
Total (without water)58,2525
Polymers58,2525
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.960, 50.000, 126.880
Angle α, β, γ (deg.)78.955, 88.541, 73.066
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 13 through 53 or resid 71 through 92 or resid 108 through 129))
d_2ens_1(chain "B" and (resid 13 through 53 or resid 71 through 92 or resid 108 through 129))
d_3ens_1(chain "C" and (resid 13 through 53 or resid 71 through 92 or resid 108 through 129))
d_4ens_1(chain "D" and (resid 13 through 53 or resid 71 through 92 or resid 108 through 129))
d_5ens_1(chain "E" and (resid 13 through 53 or resid 71 through 92 or resid 108 through 129))
d_6ens_1(chain "F" and (resid 13 through 92 or resid 108 through 129))
d_1ens_2chain "G"
d_2ens_2chain "I"
d_1ens_3chain "H"
d_2ens_3(chain "J" and resid 2 through 25)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ASNASNPROPROAA13 - 5310 - 50
d_12ens_1LEULEUVALVALAA71 - 9268 - 89
d_13ens_1LEULEUARGARGAA108 - 129105 - 126
d_21ens_1ASNASNPROPROBB13 - 5310 - 50
d_22ens_1LEULEUVALVALBB71 - 9268 - 89
d_23ens_1LEULEUARGARGBB108 - 129105 - 126
d_31ens_1ASNASNPROPROCC13 - 5310 - 50
d_32ens_1LEULEUVALVALCC71 - 9268 - 89
d_33ens_1LEULEUARGARGCC108 - 129105 - 126
d_41ens_1ASNASNPROPRODD13 - 5310 - 50
d_42ens_1LEULEUVALVALDD71 - 9268 - 89
d_43ens_1LEULEUARGARGDD108 - 129105 - 126
d_51ens_1ASNASNPROPROEE13 - 5310 - 50
d_52ens_1LEULEUVALVALEE71 - 9268 - 89
d_53ens_1LEULEUARGARGEE108 - 129105 - 126
d_61ens_1ASNASNVALVALFF13 - 9210 - 89
d_62ens_1LEULEUARGARGFF108 - 129105 - 126
d_11ens_2DADADCDCGG1 - 21 - 2
d_21ens_2DADADCDCII1 - 21 - 2
d_11ens_3DGDGDGDGHH22
d_21ens_3DGDGDGDGJJ22

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.300767955039, -0.953653802694, -0.00911382630726), (-0.953300443719, 0.300353377955, 0.0317192742169), (-0.0275118379581, 0.0182283559042, -0.999455264538)61.2500708687, 43.6688666924, 78.502833075
2given(0.974728316968, -0.22124325922, -0.0309213251794), (0.221176199862, 0.97521769649, -0.00561543122649), (0.0313973998204, -0.00136554136945, 0.999506047296)18.4227243995, 5.40111220593, -26.25171371
3given(-0.295611203702, -0.955306427704, -0.00190930173233), (-0.955307583389, 0.295612888751, -0.000664171764323), (0.00119890175615, 0.00162763380915, -0.999997956719)62.4755049235, 46.079840613, 120.213522431
4given(0.99979571612, -0.0091516576149, -0.0180214647498), (0.00946297494477, 0.999806150237, 0.0172659796309), (0.0178599589592, -0.017432989139, 0.999688507864)2.28247408753, 0.210749908799, 42.0523981051
5given(-0.483037051798, -0.875587150935, -0.00472733615303), (-0.87497134934, 0.482478725302, 0.0404897204885), (-0.0331714398835, 0.0236943189055, -0.999168771944)52.3225193667, 29.3888199524, 146.563709236
6given(-0.287994618581, -0.957626667544, -0.00320394701049), (-0.95761726044, 0.288007145761, -0.00458982546874), (0.0053180989019, 0.00174630992356, -0.99998433399)62.2261553263, 46.2635837524, 120.148297971
7given(-0.318977794438, -0.94756249013, -0.0194549210716), (-0.947756606099, 0.318838249228, 0.00997929978737), (-0.00325303718293, 0.021621705003, -0.999760931234)64.1933340659, 45.0943291589, 120.164814744

-
Components

#1: Protein
Heat shock factor protein 5 / HSF 5 / Heat shock transcription factor 5 / HSTF 5


Mass: 14298.238 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSF5, HSTF5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4G112
#2: DNA chain DNA (25-MER)


Mass: 7651.962 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (25-MER)


Mass: 7704.969 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 10% v/v glycol, 5% PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 75257 / % possible obs: 96.7 % / Redundancy: 3.52 % / Biso Wilson estimate: 39.03 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.8
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 5547 / CC1/2: 0.893

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSJan 10, 2022data reduction
XDSJan 10, 2022data scaling
PHENIX1.19.1_4122phasing
BUSTER2.10.4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→41.51 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 29.3332
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2409 3843 5.11 %
Rwork0.2129 71306 -
obs0.2144 75149 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.93 Å2
Refinement stepCycle: LAST / Resolution: 2→41.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4782 2021 0 363 7166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717196
X-RAY DIFFRACTIONf_angle_d1.181410148
X-RAY DIFFRACTIONf_chiral_restr0.06861084
X-RAY DIFFRACTIONf_plane_restr0.0196952
X-RAY DIFFRACTIONf_dihedral_angle_d27.18961593
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.907477271798
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.07545516813
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.660703651164
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.907557775724
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS1.18016328907
ens_2d_2GGX-RAY DIFFRACTIONTorsion NCS0.403117838363
ens_3d_2HHX-RAY DIFFRACTIONTorsion NCS0.657676800035
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.32511310.30412576X-RAY DIFFRACTION97.13
2.03-2.050.29461460.28022676X-RAY DIFFRACTION95.99
2.05-2.080.29361380.27332651X-RAY DIFFRACTION95.55
2.08-2.110.28241250.26822617X-RAY DIFFRACTION96.82
2.11-2.140.22981370.25372616X-RAY DIFFRACTION96.49
2.14-2.170.30211580.2492686X-RAY DIFFRACTION95.31
2.17-2.210.27331260.24582603X-RAY DIFFRACTION97.64
2.21-2.250.3421520.29622591X-RAY DIFFRACTION95.88
2.25-2.290.31691580.28242618X-RAY DIFFRACTION95.4
2.29-2.330.29621370.24752663X-RAY DIFFRACTION97.59
2.33-2.380.27781470.23452681X-RAY DIFFRACTION94.96
2.38-2.430.29361260.24162595X-RAY DIFFRACTION98.16
2.43-2.490.26351430.2372699X-RAY DIFFRACTION96.08
2.49-2.550.27851460.22852593X-RAY DIFFRACTION97.58
2.55-2.620.26221370.22452678X-RAY DIFFRACTION96.01
2.62-2.70.26321280.22672674X-RAY DIFFRACTION97.39
2.7-2.780.28071310.23282654X-RAY DIFFRACTION96.1
2.78-2.880.26461480.23752659X-RAY DIFFRACTION98.28
2.88-30.25621450.24342636X-RAY DIFFRACTION96.43
3-3.140.25781580.25482671X-RAY DIFFRACTION96.68
3.14-3.30.24441390.21022628X-RAY DIFFRACTION96.44
3.3-3.510.21571490.19932627X-RAY DIFFRACTION96.69
3.51-3.780.24191420.20532644X-RAY DIFFRACTION96.84
3.78-4.160.23711380.17912680X-RAY DIFFRACTION96.97
4.16-4.760.16731500.16312617X-RAY DIFFRACTION97.16
4.76-5.990.2151620.18372652X-RAY DIFFRACTION97.13
6-41.510.22671460.20272621X-RAY DIFFRACTION95.84
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)
14.313656740056.152792554210.01153552252619.512064396991.583030836145.94770566723-0.06607119025570.5910106016070.113745922025-1.372737103950.05365409606280.502930572014-0.08066156367660.0053365351274-0.08200012724190.4781785429090.07060572888670.00266404370990.3378782343840.03576399783880.56819118045332.9963449803-7.1477362594730.06817509
24.96975467819-3.236015612781.650996102093.57384852941-3.188826812053.57723827267-0.4555297216930.184547167759-0.733865384071-0.881010270021-0.341002142705-1.03880184658-0.55863285804-0.3844482996380.225149002150.5599542568350.03264224027510.05570311700520.226256118861-0.07997208216470.60683095972337.1139039682-19.194732672533.3435460964
36.82618065717-0.9191326719895.945679515456.169262129010.5252916997177.391017675610.340125656409-0.379085515908-0.701218641491-0.3506928485330.02857701891790.1549411107470.429540653286-0.4226524736-0.3625979642750.395092960143-0.0307630470961-0.03179935008480.2896476600860.03110494757240.60721584238731.5889689674-16.039804408739.5663440341
42.342174433232.9189473697-0.06820626735138.772828097063.327383823432.55459387541-0.3550683542861.27904000221-0.0779036695943-1.396356123380.69624865324-2.15930473531-0.3124595486931.71240966721-0.6822607826120.682020306164-0.002765906592970.131732265470.872117408738-0.0132213360771.1351674388244.1959198787-8.7137849609537.6944146967
55.91678932274-0.2637062347130.8206886595366.196960219791.777519672723.996190831320.126299280165-0.352383463586-0.2596250341840.4979502731590.06485215062590.06059730047220.236154585152-0.253942342311-0.1293165086190.2372439879710.00317549604405-0.001390238478390.2436394058470.03347674831050.3823837793529.7248085337-6.4926710702143.6815193175
65.24396015854-1.919290256630.7739144220389.39916444505-5.056977834966.95821768470.3197980642450.0384084212434-0.641871117585-0.9385695008310.2532535071731.052911501810.755619174263-1.05540807471-0.4115607564490.3589022291980.0212880439998-0.05792857859450.3824840210030.03198561119550.63113167361622.5963522815-8.2275873959333.1309565377
72.056171202041.223852002991.807019801711.486367002642.295644527463.528764489330.048359073256-0.6086491670612.46104375116-0.108235976491-0.4768221471920.554335466336-1.49943865234-0.3513179999860.7589395832280.563005626683-0.03387802575160.03799095724420.335553280058-0.03977886886170.92984897522727.88992981695.2372253695234.9424550327
85.282069954-6.37850906101-2.355494452958.312377036214.337528330347.79803591767-0.224375551905-0.974910540428-1.144346752120.4221367533660.103885211819-0.009144937431020.3061944928080.5928836938970.1537341630720.2624488199510.0379802016147-0.01114277262590.3038550439040.07468708045940.51827772182561.76847256567.8181862249446.1625310802
95.246546435630.6575767093052.198916019573.932731206315.498590318278.3061324302-0.1373963788740.136390177714-0.152886938882-0.1127628603820.416412812167-0.6314513561380.05264956775380.400680641401-0.2431460644760.1695715478060.0214071767304-0.00527647796110.2758647772280.0420865568340.41200623598166.750799347810.056650049737.8917866137
103.68393183078-2.39404393198-1.460387701866.181761568772.200693853398.13679432919-0.332107167602-1.19887843805-1.956372729740.571602829426-0.2121443596310.1911910921461.760995274790.9627384630180.2976916077740.5537914634480.07568464605940.005663328867450.5260550315920.1768754444661.0879595808956.0295588093-0.8511621351339.4179755068
112.54031372523-0.09328686595941.061606266618.235035003481.709708501624.33181110965-0.00903782883430.4580435688830.092812998562-0.2945721947470.144238577888-0.090408931951-0.1283455403570.0354839805226-0.1335250713060.2159912459910.0141314797453-0.01363561427390.1812305305920.01804027702260.27269313249558.691993878815.121305517234.0550710654
122.08174468489-1.69878174961-3.301209882275.533343135381.743091921649.0899506089-0.0770167429968-0.6509599657720.6486562104310.3951403719870.32644270513-0.0446167453015-0.2323421286280.304820334499-0.1464655297080.3804696741890.03788643711960.007553633804380.363148459427-0.01772322031650.54442740475257.853804936921.258079229946.4763984054
135.57481615839-3.281598619233.596896231878.002451163024.191496135888.85503352087-0.445984005581.80235131834-0.522234502244-0.911909180755-0.1443257512750.2101217794411.02044908503-0.8695774920310.5090142527271.40605191721-0.3044569126830.1756279621911.4912696946-0.2755133720890.5749397006351.66772452943.848589128845.35569471096
147.06128690497-0.137244998765-0.5694694834394.275379692335.421334623716.972348523460.9596587403470.1954804065120.204161046075-0.729084807643-0.651784822157-1.39475511285-0.78283981848-0.544650931829-0.1173341815891.79950745769-0.1543300327720.3449912909310.861017191628-0.1725405891171.0895616474658.038588242-5.51557605438.36768492711
156.642841911790.801497469297-1.695618728421.13229591828-1.727056790722.6592984805-0.06365566182460.853750003477-1.93677293336-1.56861006156-0.1649535652130.147470671912-0.294908332865-1.607419442580.3394980812011.72453145469-0.200409887023-0.1223978705131.08487286272-0.4191795627281.1160430649444.4915045786-6.1754450859610.7195279554
165.357281185912.843612499924.937350204449.33099297326-3.156429657178.81844506176-0.06447884053111.15156301876-1.2430811343-0.450104798769-0.489430376973-1.038427427782.515349020480.3456133087260.2630093926531.136386395250.08928452616150.1321081293830.735196529644-0.403919294790.92333295361456.3044938622-1.88500826416.6862316155
170.345655061118-0.798086447048-0.182192560013.220710050063.004005130814.76725629346-0.4627025138170.81812653435-0.959036020742-0.751127620573-0.208792464667-1.245778126990.9949961376231.77468865394-0.1452284753761.112235422340.009853532353570.445791338521.5169946175-0.3048765244220.75902345449562.92683509545.5450194261611.4934048594
187.886789710112.05981204826-1.133665296982.873994696843.166050090085.48577087992-0.6328969920981.22609271969-0.935990823741-0.4599796733350.588823919802-0.09521830728770.758006405246-0.1619551278510.07672469556920.730589647099-0.162421690221-0.02480012872510.632075462539-0.09314373182930.44170140726349.15866315055.3379494989918.2178908989
195.010163046073.04121407457-2.908416573374.990900179210.2040657199172.927237546950.1159878398430.64647807396-1.76740035572-0.3129972559881.217671596240.2156473340181.63258064287-1.92243500073-1.531040489120.92306002886-0.3641234066120.07541330077910.741826787775-0.1634032245360.92001521921245.6561000488-0.89898256200518.4946062691
201.664157323070.9208714806770.3120620112683.646716699922.362707964291.57319762641-0.124985900330.884430023713-0.620740897483-1.532063608860.7176254959791.428828741471.15116545466-1.07271629698-0.2895769276461.51231366141-0.621822690564-0.337948770021.55269516327-0.1277980410161.1641038058339.97467262090.7859794193715.99541435972
216.81635637476.687231289813.806037185088.254326373654.572952907632.55737823027-0.333369612721-0.6116553488940.781850441321-1.88826538558-0.5937023827471.47416735514-0.702570599419-0.3202980202740.950265599671.15050118634-0.434476562615-0.35473395711.624911990130.0835814086120.65964575880741.69732159699.516064517874.03563567695
228.70351077524-0.120893106925-1.180436515556.624608640130.3761917077616.30290813156-0.131103366024-0.7356085885590.1663847676430.5179823054220.144452040165-0.626028814646-0.2257397680550.03955016147770.03362256496190.4296300975840.0829499866077-0.06148839909350.388447243464-0.03994490448290.52730610459564.501385708312.489956582487.9604715044
232.331731345160.1582128629630.8430672748499.823602428344.023512188754.06868981104-0.0634930106541-0.200387511635-0.6433458111460.2019417741930.4242588824610.03423023418460.1863691965390.712965733095-0.31464359490.3255029559570.0159127379417-0.01849648086250.4634502731910.003834444119120.64305177216866.36809045766.5333710100278.3806875628
244.65114551751.875141206544.549576732986.044629742632.261480293524.521471967260.61473652839-1.1054717657-1.636294122441.981492890840.268459646261.262172862281.54525427485-1.37184910981-0.8564655528831.01772487837-0.03528446231070.1115744915740.7771252206290.1184159498111.1250339164657.91719383960.6554558999683.1647058393
258.121343007270.8502938351040.735470552248.513744389970.6597573342373.955405374450.09571194071730.290503595946-0.20892124782-0.4437010265040.0923920192742-0.118180017868-0.082238572772-0.0298905580861-0.1116937869110.3233430457040.05422583316050.006104387026130.2653464875360.01267548619550.33908978057558.837386747515.407251515776.9724432641
267.17132226111-3.13657408305-2.99803408545.02784032809-2.082285164616.76748570909-0.0789181563888-0.7366027985291.265639835970.02499180042960.583547392628-1.88914213917-1.074998040810.855493122599-0.3260375109390.405977165050.04236578555980.01552668393150.414506057186-0.09472469716410.76395085857665.281449712721.38443555184.3806896085
278.485103981214.135183593471.290915594849.16650356073.758904083659.539894915160.26233834108-0.4286101455850.1374936937230.8242443711980.2690407404191.027703000620.364004199713-0.733645799795-0.3676656949580.4487882310790.08848469846910.01937670884250.3415594390440.03874958715750.53273322032354.749071076322.279837657889.6120593848
286.16678579462-1.084933974241.224402658262.8603197425-1.730614973088.61955143625-0.08187904689760.483012926072-0.46254323957-0.5444006936730.122157064154-0.8028250368670.3720893920220.4299830698480.03584537891090.2850391892810.06041113729730.002854665918730.25261989859-0.03153375864980.39983446175936.4504410948-11.082937767874.1658541342
293.43474441275-0.4782674173655.330233877975.702453823410.718378155928.955507404430.304702509922-0.181770570067-0.497015683374-0.0597552413563-0.1068890610180.1618983325340.310571995665-0.344087574425-0.1602401843960.317453628523-0.0126521389555-0.007151984862930.176986943589-0.01542191633310.35478217102133.2067496266-14.879253767582.3450816977
306.075100563161.374287434131.819903621182.47959395331-2.207815019853.676113743260.04988145455461.2914244083-0.283698801812-1.112245126520.398725094323-1.430210108481.030029736761.12899726106-0.4107938838750.7294644119210.1368640140790.101316949620.701263295572-0.1252584926771.0644575696246.9464022968-8.4108011951479.6274819339
316.47374672599-1.73972886310.675617207325.840351215860.4019262579846.57623107399-0.0473466601908-0.0134794490498-0.2309735179870.3004371693890.0421541260854-0.01580621413310.0558113002667-0.0827180965128-9.70990456761E-50.2435814888890.01688341417060.006572400624560.15679009241-0.03091713345930.29832825278831.2707466108-4.2604807677585.8910828124
322.91769206203-1.535313874330.4614715385933.79081140315-4.816766092477.140110986580.4113449760660.182075657962-0.530650550165-0.6393216173580.3733879178190.9123440085560.599939349833-1.0492008214-0.6377828300840.4199123036-0.00364834422028-0.03798148619910.3247792846450.02358291954480.54882946176224.3715254426-7.1327773101575.7093420092
333.62751462587-2.6483049846-5.56366024194.957977349152.056102369699.914500458740.474502783475-0.4475191176493.0958761843-0.1873211241470.479711325749-0.240596978954-2.109847290240.351290566531-0.4235507777460.4734433338590.009692552587620.03524466477890.418693259968-0.06972010450421.0724636623429.84158944037.0212825905678.8124107075
344.261405384270.7218834165133.687008126796.503151966931.581300525547.519360625850.208893252024-1.250897664930.07265251656551.17447773063-0.1680789709590.6483497369740.650501712329-0.366497151976-0.1687870525240.914581442281-0.277557084765-0.1627388203790.9073793954210.1755908223360.28725828762643.5650794191-2.53834854049114.925027104
357.28209164109-1.011921222321.915801935174.963606565732.923534923357.892794755510.15964306285-0.129462733277-0.4861579387370.510428814257-0.489650143447-1.185274571360.1928239143711.316506278060.1102643323280.64142376839-0.130850510007-0.09258199769261.344807466880.1784515411110.39984316647153.3020020285-3.95390265767110.302413637
369.26441313850.667757939284-3.930163482817.865726805020.2714872980948.872960253240.276300844281-0.662658225629-1.624483033670.117963555464-0.646550284145-0.1944241583740.6576986064011.246368533010.336365037720.631105181110.136329451896-0.133068383570.8426958169570.1096062582770.72227778690748.0218636111-8.47521930763103.131670818
377.890798239221.69762980869-2.607137672364.18031836234-3.869969984527.0619420070.433335948679-0.990391492092-1.021285093651.00359886077-0.735092756877-0.4052842467261.06853332638-0.349653005440.142315477490.600641492863-0.188321724844-0.03595178268540.534898566660.08898062605950.33976735432938.1534517187-5.56318083948103.82443051
383.47029494418-1.496432561182.656055694214.04342435751.199215571656.694659780860.586771426549-0.2761984740160.3505078732740.53751477752-0.794110070095-0.762108200129-1.15580351021.483534233460.1177648635770.864844208071-0.3517807972610.01607584900360.9934577745210.03934663758470.4044485763448.81933562355.10363420074106.533205518
391.836396909810.37767654210.9209904000020.355275164460.3391111559840.5948951238230.0787251254021-0.5676839097950.2372629430080.268033355997-0.2507549699410.36653220075-0.488953957112-0.20456084463-0.04007139271861.30522491628-0.335617453003-0.1604093069040.877836869627-0.293394992345-0.73609682101840.67017866838.58173373153115.441676507
406.322624562122.16566439359-5.349287965741.98221069685-1.576751628814.290720372310.0100980866841-0.5162674503110.5066038225320.2602271825870.08847370375470.0385898536202-0.01943145219510.43731254202-0.1250152126660.2577452797340.0688916536928-0.03095057618390.233915657314-0.005022893308610.34320936676236.9849619273.7519096152345.0048054205
410.4821568540411.28400933894-0.3425669157813.35965133145-1.156529246520.4141553034160.2539886182260.626506716180.47138553838-1.034865579680.1962030041920.556232837210.02635618158011.11280191833-0.3671269727030.575122350292-0.07069096532640.006102203766190.9797351812980.1480809326670.36093742736354.992059282522.533776460513.3797419179
420.281981753242-0.4250952426080.06326366857252.19949163427-2.033032155492.4068234222-0.2199312517021.089210691660.230735675611-1.114401177270.5728890059590.0107834608071-0.828441951471-0.245088697484-0.1061929527630.926956156742-0.1970215124880.02110143414010.8769198747690.163930247680.34471974878655.189090048722.334759950412.7723024187
434.371208039122.13725265331-2.385799231822.78130765826-1.73663583963.143414487120.12068081265-0.3184836450560.5601141791050.1534613655490.09715043412390.385866698034-0.119784401785-0.178385816474-0.2586822588930.2222192861090.0554561359928-0.01607261866440.295794785409-0.02345459569990.52375982280936.98047318386.7016545189644.3540108494
445.81143427534-1.83220606284-5.223834552786.00739633255.499014267747.572724892270.2369221663340.4705222934720.359927668843-0.7650205315530.355725239348-0.8349954273212.463684335771.29434970589-0.2672275112860.8093073842670.1809188722820.05207288032770.4368260159670.1098402994040.43807707288259.023553767716.570446497763.8317214031
452.116976354212.66601690047-2.80689085933.47951592211-3.686326704273.84778508723-0.0724751498681-0.1049299369671.10728720021-0.3208681178420.3955978963051.793968814890.0661116758503-0.341094376948-0.4460463665720.3831137314410.0517232634035-0.01009800700510.4174561961930.1314969424640.73921777428643.03816959714.530353887473.3468369294
465.051085816741.66856614811-2.343681588091.79944565943-0.5416778290786.163088150410.251454972904-0.3104933772940.3283942787110.233970856908-0.001452253925330.308565014704-0.160817633182-0.180028393148-0.3642638652660.3507831125440.000489276303470.02737360621420.2774975545270.009740385754230.44149045570434.19401270234.5327071609493.9999331872
470.277962993818-1.123794362341.20935709798.72884262001-3.108386197316.024052464750.0299518222014-1.810946509750.04159459823081.843292609211.149272492371.174545597512.23592344998-0.595609194774-0.4803799993181.38804164125-0.2918454433260.1682254686772.022589428620.02834987499470.64820916760122.8407815532-4.87955938028114.944971853
480.278138119289-0.9651954574290.2115975381524.45940413545-1.010558298780.2087816603170.765583478718-1.395575944510.2812111566671.47574970567-0.33607228211.30480877994-0.907291942478-2.50138463747-0.08706938904920.917269910749-0.2669245625740.4079138004631.57300534418-0.08656766409650.52261117904224.0881895782-0.0909229918036110.343731004
494.935792970653.55080454467-3.66217717884.15775802687-2.609194391984.136835226910.1363196610920.2302011009340.731604759705-0.1714848005640.3019716551460.320230703059-0.191391322043-0.0256061289945-0.511042031340.332629113520.0507209199046-0.02823680559350.2860747604370.01913166149160.48581055394244.006487352511.824058384476.9347402296
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 11 through 23 )AA11 - 231 - 13
22chain 'A' and (resid 24 through 29 )AA24 - 2914 - 19
33chain 'A' and (resid 30 through 50 )AA30 - 5020 - 40
44chain 'A' and (resid 51 through 76 )AA51 - 7641 - 51
55chain 'A' and (resid 77 through 108 )AA77 - 10852 - 72
66chain 'A' and (resid 109 through 126 )AA109 - 12673 - 90
77chain 'A' and (resid 127 through 131 )AA127 - 13191 - 95
88chain 'B' and (resid 11 through 29 )BB11 - 291 - 19
99chain 'B' and (resid 30 through 50 )BB30 - 5020 - 40
1010chain 'B' and (resid 51 through 76 )BB51 - 7641 - 52
1111chain 'B' and (resid 77 through 112 )BB77 - 11253 - 76
1212chain 'B' and (resid 113 through 131 )BB113 - 13177 - 95
1313chain 'C' and (resid 13 through 23 )CC13 - 231 - 11
1414chain 'C' and (resid 24 through 29 )CC24 - 2912 - 17
1515chain 'C' and (resid 30 through 37 )CC30 - 3718 - 25
1616chain 'C' and (resid 38 through 50 )CC38 - 5026 - 38
1717chain 'C' and (resid 51 through 76 )CC51 - 7639 - 51
1818chain 'C' and (resid 77 through 107 )CC77 - 10752 - 72
1919chain 'C' and (resid 108 through 112 )CC108 - 11273 - 77
2020chain 'C' and (resid 113 through 120 )CC113 - 12078 - 85
2121chain 'C' and (resid 121 through 129 )CC121 - 12986 - 94
2222chain 'D' and (resid 10 through 37 )DD10 - 371 - 28
2323chain 'D' and (resid 38 through 50 )DD38 - 5029 - 41
2424chain 'D' and (resid 51 through 76 )DD51 - 7642 - 53
2525chain 'D' and (resid 77 through 108 )DD77 - 10854 - 72
2626chain 'D' and (resid 109 through 120 )DD109 - 12073 - 84
2727chain 'D' and (resid 121 through 131 )DD121 - 13185 - 95
2828chain 'E' and (resid 12 through 29 )EE12 - 291 - 18
2929chain 'E' and (resid 30 through 50 )EE30 - 5019 - 39
3030chain 'E' and (resid 51 through 76 )EE51 - 7640 - 52
3131chain 'E' and (resid 77 through 108 )EE77 - 10853 - 71
3232chain 'E' and (resid 109 through 126 )EE109 - 12672 - 89
3333chain 'E' and (resid 127 through 132 )EE127 - 13290 - 95
3434chain 'F' and (resid 12 through 23 )FF12 - 231 - 12
3535chain 'F' and (resid 24 through 37 )FF24 - 3713 - 26
3636chain 'F' and (resid 38 through 50 )FF38 - 5027 - 39
3737chain 'F' and (resid 51 through 86 )FF51 - 8640 - 58
3838chain 'F' and (resid 87 through 120 )FF87 - 12059 - 80
3939chain 'F' and (resid 121 through 130 )FF121 - 13081 - 90
4040chain 'G' and (resid 1 through 15 )GG1 - 15
4141chain 'G' and (resid 16 through 25 )GG16 - 25
4242chain 'H' and (resid 2 through 11 )HH2 - 11
4343chain 'H' and (resid 12 through 25 )HH12 - 25
4444chain 'I' and (resid 1 through 5 )II1 - 5
4545chain 'I' and (resid 6 through 10 )II6 - 10
4646chain 'I' and (resid 11 through 20 )II11 - 20
4747chain 'I' and (resid 21 through 25 )II21 - 25
4848chain 'J' and (resid 1 through 10 )JJ1 - 10
4949chain 'J' and (resid 11 through 25 )JJ11 - 25

+
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