[English] 日本語
Yorodumi
- PDB-8qtt: Crystal structure of a C-terminally truncated version of Arabidop... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qtt
TitleCrystal structure of a C-terminally truncated version of Arabidopsis thaliana 14-3-3 omega in complex with a phosphopeptide from the inhibitor protein BKI1.
Components
  • 14-3-3-like protein GF14 omega
  • BRI1 kinase inhibitor 1
KeywordsPROTEIN BINDING / 14-3-3 / brassinosteroid signaling / phosphopeptide / transcription factor / signal transduction / kinase inhibitor
Function / homology
Function and homology information


brassinosteroid mediated signaling pathway / plant-type vacuole / Golgi apparatus / mitochondrion / nucleus / cytosol
Similarity search - Function
14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein
Similarity search - Domain/homology
FORMIC ACID / 14-3-3-like protein GF14 omega
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.35 Å
AuthorsHothorn, M. / Obergfell, E.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_205201 Switzerland
CitationJournal: Plant Cell.Physiol. / Year: 2024
Title: Mechanistic insights into the function of 14-3-3 proteins as negative regulators of brassinosteroid signaling in Arabidopsis.
Authors: Obergfell, E. / Hohmann, U. / Moretti, A. / Chen, H. / Hothorn, M.
History
DepositionOct 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _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: 14-3-3-like protein GF14 omega
K: BRI1 kinase inhibitor 1
B: 14-3-3-like protein GF14 omega
L: BRI1 kinase inhibitor 1
C: 14-3-3-like protein GF14 omega
M: BRI1 kinase inhibitor 1
D: 14-3-3-like protein GF14 omega
N: BRI1 kinase inhibitor 1
E: 14-3-3-like protein GF14 omega
O: BRI1 kinase inhibitor 1
F: 14-3-3-like protein GF14 omega
P: BRI1 kinase inhibitor 1
G: 14-3-3-like protein GF14 omega
Q: BRI1 kinase inhibitor 1
H: 14-3-3-like protein GF14 omega
R: BRI1 kinase inhibitor 1
I: 14-3-3-like protein GF14 omega
S: BRI1 kinase inhibitor 1
J: 14-3-3-like protein GF14 omega
T: BRI1 kinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,34531
Polymers278,82220
Non-polymers52211
Water6,648369
1
A: 14-3-3-like protein GF14 omega
K: BRI1 kinase inhibitor 1
B: 14-3-3-like protein GF14 omega
L: BRI1 kinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8566
Polymers55,7644
Non-polymers922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-29 kcal/mol
Surface area23440 Å2
MethodPISA
2
C: 14-3-3-like protein GF14 omega
M: BRI1 kinase inhibitor 1
D: 14-3-3-like protein GF14 omega
N: BRI1 kinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8566
Polymers55,7644
Non-polymers922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-28 kcal/mol
Surface area23110 Å2
MethodPISA
3
E: 14-3-3-like protein GF14 omega
O: BRI1 kinase inhibitor 1
F: 14-3-3-like protein GF14 omega
P: BRI1 kinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8736
Polymers55,7644
Non-polymers1082
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-31 kcal/mol
Surface area23450 Å2
MethodPISA
4
G: 14-3-3-like protein GF14 omega
Q: BRI1 kinase inhibitor 1
H: 14-3-3-like protein GF14 omega
R: BRI1 kinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8566
Polymers55,7644
Non-polymers922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-28 kcal/mol
Surface area23010 Å2
MethodPISA
5
I: 14-3-3-like protein GF14 omega
S: BRI1 kinase inhibitor 1
J: 14-3-3-like protein GF14 omega
T: BRI1 kinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9037
Polymers55,7644
Non-polymers1383
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-32 kcal/mol
Surface area22910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.216, 71.082, 150.986
Angle α, β, γ (deg.)100.470, 95.530, 88.740
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein
14-3-3-like protein GF14 omega


Mass: 27139.514 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Col0 / Gene: GRF2 / Plasmid: pMH-HStrxT / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): DE3 RIL / References: UniProt: Q01525
#2: Protein/peptide
BRI1 kinase inhibitor 1


Mass: 742.710 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Col0 / Gene: BKI1 / Plasmid: pMH-HStrxT / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): DE3 RIL
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: CH2O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02M of carboxylic acid, 0.1M MOPS/HEPES-Na pH7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003353518 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003353518 Å / Relative weight: 1
ReflectionResolution: 2.35→50.33 Å / Num. obs: 118395 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 39.59 Å2 / CC1/2: 1 / Rrim(I) all: 0.217 / Net I/σ(I): 5.5
Reflection shellResolution: 2.35→2.49 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 0.95 / Num. unique obs: 18838 / CC1/2: 0.51 / Rrim(I) all: 1.856 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.35→50.33 Å / SU ML: 0.3991 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.3187
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2755 5905 5 %
Rwork0.2345 112213 -
obs0.2365 118118 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.72 Å2
Refinement stepCycle: LAST / Resolution: 2.35→50.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19077 0 34 369 19480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001819503
X-RAY DIFFRACTIONf_angle_d0.406226299
X-RAY DIFFRACTIONf_chiral_restr0.03562898
X-RAY DIFFRACTIONf_plane_restr0.00343418
X-RAY DIFFRACTIONf_dihedral_angle_d11.10787342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.380.4151880.37533603X-RAY DIFFRACTION91.93
2.38-2.40.38611900.37143618X-RAY DIFFRACTION97.17
2.4-2.430.38531990.36983763X-RAY DIFFRACTION97.51
2.43-2.470.38141960.34933718X-RAY DIFFRACTION97.44
2.47-2.50.40211950.35143703X-RAY DIFFRACTION97.52
2.5-2.530.37091980.33553750X-RAY DIFFRACTION97.41
2.53-2.570.39571950.33683686X-RAY DIFFRACTION97.27
2.57-2.610.38881960.31793720X-RAY DIFFRACTION97.75
2.61-2.650.35041980.31683749X-RAY DIFFRACTION97.75
2.65-2.690.35471960.3153712X-RAY DIFFRACTION97.26
2.69-2.740.33911980.30563764X-RAY DIFFRACTION97.73
2.74-2.790.3631950.30313706X-RAY DIFFRACTION97.79
2.79-2.840.32621980.29793786X-RAY DIFFRACTION97.81
2.84-2.90.36641900.29573661X-RAY DIFFRACTION97.42
2.9-2.960.34582010.30223807X-RAY DIFFRACTION97.9
2.96-3.030.31571960.2893721X-RAY DIFFRACTION98.29
3.03-3.110.30542000.27443794X-RAY DIFFRACTION98.16
3.11-3.190.32291940.26873691X-RAY DIFFRACTION98.21
3.19-3.280.33932000.26563802X-RAY DIFFRACTION98.6
3.28-3.390.30611990.24893779X-RAY DIFFRACTION98.42
3.39-3.510.2831950.23313724X-RAY DIFFRACTION97.9
3.51-3.650.28751970.22683738X-RAY DIFFRACTION98.55
3.65-3.820.24861990.20633763X-RAY DIFFRACTION98.61
3.82-4.020.2111980.19433783X-RAY DIFFRACTION98.64
4.02-4.270.22571980.17243761X-RAY DIFFRACTION98.75
4.27-4.60.20471990.16693793X-RAY DIFFRACTION98.84
4.6-5.060.22742010.16993817X-RAY DIFFRACTION98.92
5.06-5.790.22971970.19573739X-RAY DIFFRACTION98.92
5.79-7.30.23532000.19373792X-RAY DIFFRACTION98.98
7.3-50.330.17541990.15913770X-RAY DIFFRACTION98.66
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)
10.3934200267320.8243557051670.3600107461632.4649823042-0.0003033041442541.220072917560.0657280493467-0.1701898595470.0674558706680.443884607722-0.0804333009940.2679965661870.248307363039-0.286753178390.1407723449950.1969486125580.247604062543-0.04361169790370.300574263225-0.04036617687730.50002773087937.926744704657.535775739521.2513549875
21.021498645810.1735975397240.5398833620681.83609327841-1.044236143141.53431001265-0.04538219805250.00407093624597-0.02224890787820.08620071193790.00721684334185-0.1212731801360.1451942794010.232120764616-0.03008197007710.450029813902-0.0710799707730.007830923566820.400857109179-0.01685668187720.27817193931950.624801873938.726277766319.4338243896
31.44610695991-0.5683327179650.1664469315521.77753926416-0.277774421391.228752910920.2515306588350.135250450108-0.181956637398-0.0614980035636-0.2158321417170.5995420585850.324674489556-0.3871790506750.1895433469980.403374862578-0.07029798387730.02726701110140.446679795827-0.04010882501550.35880524538230.686459631733.39113187319.536979591
43.76007422154-2.21504722655-0.2210379285513.64084423109-0.3610332524840.7362354673570.3748596461860.494946869830.321528393813-0.641521210783-0.4591384372460.564079023796-0.233864032927-0.4666481026940.1410395741780.614376145887-0.0247564657361-0.1280250589350.6288589261370.04306530629080.45516165489830.523212512434.97220033994.67717945347
52.115950678922.118072655930.3486530800032.37700490460.5348552463090.228493982672-0.08924784171050.0835971140001-0.5159518865240.00289999533123-0.132209618582-0.7601295850870.2396223339180.5638222329150.05483624338460.47317216047-0.09755209251270.03012471425480.700213476690.1630078857390.52439132347569.414918605645.117211317613.1988526154
61.584783599320.58270864182-0.412984623811.52397905419-0.09068027413462.28755509423-0.0329458909047-0.107111548461-0.0520463386658-0.0960474138899-0.0762975571253-0.023783697473-0.1965522849820.379403210161-0.3175228360130.38402039071-0.116996070461-0.04304403211580.4656943588130.05338763659010.33292203370260.099314825662.1938113768.5830301408
72.178253043020.4125483661020.4111085127321.33989808849-0.7427333583551.597204951270.1712265525590.185980976153-0.0947178138188-0.394258964424-0.147327446422-0.108131595179-0.08988146382770.111661019277-0.03690958571220.605614712835-0.2149414994980.0197599621330.6372683510250.02323314229780.35349058806869.003550591963.3583083738-8.79624268818
83.28120694607-2.58417618619-0.5709180186934.199549736570.1392471104391.859390297160.0230984929010.685623416765-0.747009782348-0.776124432849-0.1434339838090.6398970542190.2049892727450.032825036856-0.1517650217240.636880553033-0.327790869977-0.07911448636160.760822945214-0.06414268006940.471253640759.021811028558.4241082645-11.9835403547
90.4246855429670.2237787869730.1599221702240.2039968361140.3347712365980.8797358192220.180729285556-0.366725916509-0.3984894337880.259811966617-0.2040774666860.03177081663270.634248952348-0.319010263561-0.07614785881110.3199786078070.000878164970939-0.05156306780390.3288974865650.02572186796470.3767012229430.880397428810.7682688638-4.64597564217
101.714297179890.9843789041440.2596359616891.400790385250.4211150627980.777942952537-0.1315656297480.2817661035910.140746785184-0.1792071195590.114963403630.2876505232060.0972198414903-0.211130594196-0.1630927759370.320052343048-0.112380808557-0.05713656458180.4804584361470.01501496618340.34120410252912.656152675816.2997942105-13.5386919595
111.158794932050.5466822540080.1402009125511.45849750324-0.6729442800441.836779326380.28523078696-0.7124207842440.3881562048430.466181411252-0.3466848281990.472215226177-0.132204262111-0.622647849119-0.1203550802930.482311504276-0.187295773550.01076251350390.681338049335-0.04381996235420.3611697727625.5115461731610.43373442452.3984764395
120.6127137470380.515457754996-1.249152088642.117507929130.09261321852423.33113383515-0.0652326766356-0.8139208627760.4388692220730.7622815683460.226968831378-0.410806559320.003566658312320.2998104325350.2619715654230.845433177075-0.164946908360.007899028936910.939959173289-0.3264817999860.6353233086111.197857667521.54926436615.1008095252
131.599205856890.335060282684-1.884515869571.30620760434-1.230513258132.794484168570.04121359060080.07176019499880.3051652459220.0667761106467-0.2866957609590.861390976504-0.215141018733-1.146565871330.1412379927620.5077303598020.04756095961820.08456268610930.731861881317-0.2321243593930.7639176758025.8576909802723.21285486941.76413349156
140.235074401757-0.2488400110250.3372449042740.753530470494-0.7152133913191.16728384119-0.1651112219060.2080619003680.278030858208-0.2144942163530.227271229880.117005583935-0.0861522310299-0.1819300322280.05471571075110.600483989921-0.222548247118-0.1139433480330.7733961196050.1052302510960.57089360858116.764269260929.536051675-28.9755074283
151.48489889677-0.0395677930821-0.222537212342.052262757640.1069163950161.65748754431-0.03715417919770.2193479853150.150883009474-0.176420838993-0.0198007830783-0.323559389064-0.008519722820990.1464122426710.06269600958970.371031431524-0.1446672381230.008433336184260.4564003192830.06368043793230.37869854847434.861965834628.5135764112-17.587712025
162.248099176532.053939240230.1045233657492.03637566920.6001631535911.96257938361-0.2812552548520.1880867008460.123035966375-0.3919180084820.258397657146-0.0896679215492-0.292636617582-0.2348471753940.3031305266330.634616587705-0.2622174409610.006268467263780.6823061286280.07051478057570.38949882461134.241553091939.8879758839-27.9665384859
172.04978427173-0.39048721690.6960107052132.25341199332-0.938873030562.02088639696-0.0947905873619-0.5756537154950.4341237936430.4517358987210.1339968063330.403294933227-0.933268552977-0.1438085782090.06034308113240.755335099248-0.2045553999360.06808379374420.696446816270.04909937571940.56061423430635.243884758251.0349083961-19.2231373281
183.14887268215-0.6023653221213.424316355530.77408360864-0.06668788469354.24642215713-0.005848731044760.535085056996-0.3286958224491.108328110590.1373849888650.547933693589-0.8316188309750.5116956178790.1884886334940.736031525801-0.2027908937190.08034490270620.625127238356-0.05210823952050.56751260323132.561976063544.5587677762-11.8092830986
190.04813660619930.41341491193-0.08206660859564.72070931769-0.121248489691.448784428370.1089076076120.33983683018-0.1711442535250.00820353272516-0.536763430507-0.581704950926-0.0300281838420.495321018269-0.1328143604960.687261769197-0.1608007025060.1386980262280.6409274719090.017077566210.6074442368632.5705715045-2.8392151603855.016413177
201.745026317381.211119482520.2330554667491.62031855024-0.2498210291091.595799796190.0636258190605-0.09451781843130.08077463252890.222149305198-0.0820068232868-0.0294029522096-0.07979724549560.114772143482-0.04634393250830.574234945951-0.120675792910.02683725837210.416679666604-0.01149275198010.35538125304330.126468291816.029798718564.1257445077
210.3915149877270.05355261812050.3008935061210.214996340161-0.1169840291230.3915528197580.0527571138544-0.120467731893-0.01152097219440.0722395710737-0.0985089964265-0.2069862621480.02139440200070.04226683706810.07103836679240.494991743233-0.1385743219880.0522943705120.444529257555-0.02977000213940.38687459389639.308819187518.848745996753.5027839274
221.749959020680.03194616004190.3283526866620.994388843565-0.930601033320.840117627244-0.2244115332260.249890700930.141045239966-0.08162078707390.06601083830660.372015373863-0.0644621960175-0.1279664843010.02555283590870.573277525631-0.211390080961-0.01774301032990.503932057843-0.01430313154830.37717200315634.117664414426.880713854144.3390810903
230.604037278426-0.365194129186-0.2579330613023.347060259363.618898406194.742547325550.102767520450.2992643080480.204740851196-0.798626524801-0.003405350365880.629691063063-0.554815682517-0.834260095778-0.4055706395550.600747308071-0.289424080089-0.07668924691290.825621433890.1084533827820.53400192704622.628095372724.995254890143.9079550471
242.71756074196-2.37519008784-1.167815160253.244290414012.152991495082.43629554340.113259394545-0.4049738148910.20637432787-0.05663884326030.232342046250.0446352673628-0.168254269798-0.205015126527-0.0911254754060.495205526062-0.1732003904210.04769057328250.435039482836-0.08697750421130.42267006923615.730325718419.415262783180.3820329499
250.1930822748560.206981580374-0.01371084944770.1622110143960.02827495164330.0195476815034-0.07280935121190.0263333667281-0.08678148286980.00892083630853-0.03478727676620.2177817672360.11241174073-0.1108254238470.03152650159280.585851639857-0.1872870930590.08764909237160.432486535018-0.04034083479210.36897326340414.37467625523.8710142774572.3641597181
260.3320537329710.0495472229441-0.1867346134870.2793766077070.04175358853910.1692653944730.000179525263998-0.49339293038-0.1773982621490.162544086696-0.014088659486-0.09092878462930.04479907699990.2552494436560.03685706848640.557689461999-0.1927236750620.07439170535670.4791882357670.03418139891950.42414018204518.5260756883-5.0257585372573.0020487442
270.1318879433640.0304098699379-0.0696503026590.1552176084190.03299811157410.506071806427-0.0541509351352-0.159717880547-0.127489181807-0.173313589774-0.0303304425836-0.003825738020190.274200149088-0.2075766052280.02337927487240.603046946086-0.2576194909290.1032175786580.5412546253540.03689257792590.3611040888383.72594618044-6.2729346827377.742982701
280.1722266013860.01855618473590.0661497379160.04859369897830.05291448966150.0730341984313-0.05466102889910.1993930145910.338781437109-0.3108050536540.09438796736480.0684077383040.122878306437-0.311736139964-0.02051518188860.58826165825-0.2153758877420.07549406541010.6584062119460.01628777642470.372280772396-4.6013165173-1.5377577869571.8590514085
290.0353211215771-0.0151725309380.0105778737653-0.00402431164923-0.00194998575671-0.00804245444539-0.08272145375180.156636547722-0.2863647703930.0152880103664-0.1250879987630.3089371245310.232465892007-0.0743914164549-2.13942213499E-60.743643694772-0.383225455032-0.03824149491730.902858301584-0.009225251115350.50774061991-9.11352500359-6.9256447925567.024477785
300.0005609583587570.003598613464460.0001643017915920.005502975941380.000775578115357-0.001939007214530.00135300591604-0.01639259721170.1658069116260.1440694241320.00207502794238-0.0844903989241-0.0504599952747-0.00741377954909-1.79729943392E-51.2410704015-0.03327634813480.08115608850861.510403172650.007231530334720.876394985521-15.351241024213.469168302571.6695608266
310.7815439778130.04967254259840.149344577190.196353517190.02606011168050.03856282918870.3032867852950.807190711013-0.0391453855733-0.6848186183460.0595007314174-0.0656521561842-0.265199565569-0.2895996914250.01587686909140.843048089134-0.156672860281-0.07649568790670.7501224751450.2072806588540.319353168758-4.589004902542.2593563514962.4750544252
320.349202592138-0.1776313447120.2444114195890.0980554227104-0.1311090014440.2665149311850.2842752748330.6368985292470.3365052104810.1578890443070.247300396663-0.0569473868413-0.207675354889-0.09654646320340.4242121979940.1541191576430.4757005310630.00947033657207-0.03600728060420.06021586444310.530899667547-12.3783466737-4.4024160366930.5001160119
330.1900608427220.141075067594-0.1965024729680.141165522178-0.2442195417920.185874139530.00636140443543-0.2952346796450.1225818281380.291684811190.0051879613079-0.0168833854004-0.3128312923120.164508775971-0.005999301110310.29258169607-0.038383205179-0.01862175449840.3484292538910.02315803729630.3059584548675.48772111638-14.943469850736.2857669325
340.3287360660740.09502114407070.1148588617730.125175823809-0.06930277260940.3894432904320.1476145090520.1527002955710.117386995409-0.0734034551822-0.0393511671337-0.21216734908-0.07610840316190.1037898123530.003936194752270.517873453179-0.1060187777030.06895229610880.4835388860590.05877408288980.4155159921376.64089468009-10.58200766628.1616338788
350.6674619965320.1579011678730.7438840697960.2536527967720.1314707440691.31228693605-0.0213066934760.3933495718240.75775057255-0.1616709262360.0668648292975-0.0207265312544-0.3097195659410.2522346905020.4404603887250.541120309229-0.2608127806610.07372966529550.7450048421380.2053404494570.72024523505414.93872356741.0213770775827.1816789452
360.108532460579-0.1412362593340.1597158938220.169952274007-0.1761832043560.287718729899-0.07684390556940.1528174786590.249453179501-0.266443811432-0.172899165021-0.0333731658686-0.09120080047710.366194093958-0.02165132139450.606925406925-0.1856330676210.03351294534310.549468577843-0.06943211136080.68764290271213.99615953242.3978152052637.6661096712
370.245852123431-0.123249014056-0.3015895742050.177655447962-0.006679429060690.5750715394-0.3535057828290.0600715077450.2768086202710.182253350771-0.08028221862440.0479716314854-0.2597196140230.27787140378-0.06498565321630.658904435833-0.273755407851-0.1814736113360.616441419886-0.05627495397710.92147575815415.54815133549.6844173817944.724894671
380.01767308093040.014657481776-0.02588087975890.0640753834657-0.07006677656070.04720880878760.0930246893905-0.2432077992320.313403462190.1894551025820.04028319459210.0718401613016-0.187533257568-0.08616072159780.008596260668690.800184331169-0.1211397854220.05293279628090.598782696338-0.2038435350550.652711827710.54775953153.1864237415648.7518370155
390.0143248201355-0.008481147451640.00716062177988-0.0114586313824-0.007834249421240.00114275647640.079055649741-0.0810562195359-0.1272802680850.332835172077-0.06321030168430.1079603498690.2889747823860.186003309034.37212601161E-50.599901942656-0.1876343071550.01204842101570.5731259103960.02124221096210.42662552565313.7351097667-5.9595246532144.5917022693
400.02417409469650.00165800399761-0.05330496606720.02692888645280.00841450938970.279955351559-0.0480434453734-0.3188891503-0.0262291373441-0.0884631786362-0.0330834218188-0.3737577958090.407793963097-0.164114723683-0.04661490882810.337279156862-0.01286415594560.01186099593970.2988563453320.04941256287460.3314304512060.435356670303-33.967123844837.0754007883
410.5011363293750.163899038872-0.08650310580260.446806433006-0.2284762922080.0580769326156-0.0129129556941-0.735082605848-0.1568802260130.7161506428430.00143504602037-0.110488102543-0.04566047786320.02681000388790.02335508081840.397912596303-0.06851416461590.01579374833120.3156723050060.05804712708860.344294555543-13.0720857869-25.829412443.7938568012
420.6810860018550.349879327076-0.07524244304040.411105539633-0.06809289640580.3389481682410.287318309258-0.203439957201-0.0103705133004-0.0662718365284-0.1755722319140.2146776435420.106768481783-0.1381594275150.2978847509450.3658351671410.02056767949490.06731247840080.217952568945-0.03561307166110.414396694171-19.5405718753-26.204482288937.9635620247
430.7294396097320.02472435129360.01104922003440.76914206251-0.2046719118440.02210319207440.275119279045-0.06662877153470.0899787065140.190998658869-0.2826694408610.1304723113280.164586930907-0.0713132091722-0.03739060417380.520504253028-0.213384509661-0.05078881911790.444063791340.02831582361510.283214117607-21.4297627854-36.680278505849.1649059863
441.377786077380.208908046481-1.01308687550.9858651587160.04429376626290.9754130319350.631438112306-0.1946153884380.0503130508660.241022521064-0.5346531606880.0280288098614-0.3844597695580.254715006880.4675257825740.506000040628-0.241414171142-0.1127255806310.5271583570380.06815878756160.200376335011-18.5268361712-33.811491160358.7554722133
450.027813307933-0.00205798077378-0.06696318984190.08354280983780.04863602979550.1905695247290.133093577798-0.023521307097-0.1974617343810.462344561518-0.0698473406042-0.05247985289790.020062841668-0.3656676538040.01084849969051.16509399086-0.482665510566-0.08864386034580.8903305152350.1367234515460.465149063899-19.1227126798-34.304796599468.0315446454
460.07143430047180.1300599982620.07998677113730.2016287776470.1311803269580.1364514701120.0497155475784-0.5079922916920.1545868012570.4795598678720.0601865082212-0.4064915487530.1405598913060.264955780563-0.2141565806610.875140742629-0.996569561927-0.7835763925940.857136306746-0.208437256019-0.0131626865596-12.0570418465-27.039847120963.5681332155
470.26223795223-0.02034970101260.001860855762460.0513895848423-0.03602743539090.01691336941140.129709563394-0.1038033049740.194495287751-0.0452163829551-0.0754326779669-0.0208865572174-0.246277065008-0.185177420351-0.004963846813920.625770002578-0.1968123625880.02996313845730.5442130659880.002686136026210.265860831795-0.8506086850696.40051877222-39.2319806975
480.01705721535890.1713109794040.06899438386070.02484811230930.007339869921910.07006948380120.06657696642090.04978788335610.08217315493170.167723721525-0.118243050095-0.1394505787940.1186177303940.3832530443880.008567978874710.740121504667-0.2839041971840.08806330591740.562181707688-0.09342025272130.0397119292581.187194676440.70795553619-54.8438070572
490.178853684328-0.212942242812-0.1593895733490.810243147570.0997716123160.1270419859090.1539969768130.2031091884770.193170281875-0.03071265931720.0116662901632-0.1179090480730.0413124409935-0.1480710148570.2048707990960.642201489571-0.2654785983840.04399366192050.5135307175250.00501170764670.2410705638190.3780565863016.34206455103-59.3426560194
500.427392707063-0.229086304345-0.05895283453860.1361920368130.005850091867140.07757746198430.1106865203750.2645237681170.119713293071-0.121507061064-0.0371749588739-0.0195742176572-0.1405074811870.239851476560.05583509120920.64673401443-0.2457482623020.01652231106670.4782722141630.02601910822570.35139720588512.854060299611.6414741195-64.1942777431
510.206966493032-0.1171076641420.07151166902820.09293783942620.0158620032220.105526819926-0.246983377207-0.176019756263-0.1295767223610.003015487320830.296225521658-0.0818507808525-0.06723086986670.0921055794587-0.003255078206910.622786032713-0.249929667510.04511922718910.5307102567620.00521820214580.42065990369118.64928841643.0454851001-58.4194743907
520.100922374327-0.0101408964130.02867458148060.239418368635-0.07953251291810.0514703028911-0.1222331069620.135276216454-0.0834451494401-0.376001237589-0.049173099825-0.598480982585-0.1880100638850.184111451187-0.02062214029960.809573523693-0.1742654965980.1387877754670.611203234727-0.04017428561590.64166589329525.3760422746-0.58030439366-59.5805091573
530.0236606234346-0.005240826232360.0270716796053-8.51121461616E-5-0.006969733215510.02304847017280.0264550250242-0.00535029848998-0.3021165532840.113099476505-0.272831351927-0.2125219392150.2278437030870.205903246614-4.50328975748E-60.773791263815-0.1815959939630.1559247401460.395782247284-0.08621687760630.73542361326521.2883079912-6.47210492096-54.3164034076
540.0514064103571-0.04303822725830.01999989981610.0216132349593-0.006998875782120.00605417620696-0.199886741286-0.263140460969-0.199995438707-0.0794621678277-0.287256347469-0.08882565801420.06803985356140.00827155452156-0.2047179783950.5737991426-0.2909997746740.09205734643180.6824586667350.1918772852680.50407979063613.0568157444-7.28576597036-60.5816098458
550.1138110144340.0909699666218-0.03281739562970.0191902614777-0.02622815339440.0309066288544-0.1121929898430.0638347148743-0.0571057706727-0.1335469941970.125610820717-0.0116714932517-0.1299537981350.04854634273990.01880481568920.577845943499-0.254670616636-0.00723841061690.5693665799540.02268502713240.221910306398-15.0867950495-12.0927402635-48.0566091658
560.129661343955-0.2010682701960.02525015314160.350859391063-0.1440819606470.128269552355-0.000194376979130.03910212766410.04925635812680.1054263157880.1340723610180.095231540895-0.219201191599-0.02147315647490.001034206048380.52563202485-0.1846340584990.005582745342330.5957342125360.01405484920340.287258956688-17.2962338248-7.15462955445-36.2779827206
570.0596784844440.09717228368440.01409903991170.169039886482-0.04385899387130.1401308490180.137163379542-0.132625698786-0.00997278028203-0.03346342469140.001486993193860.0973045392782-0.0368045317001-0.133448874911-0.005544684242960.469564856641-0.232130101945-0.01080958846820.5978525364420.07144562030730.31230859019-22.5585894186-21.812637075-35.0231077507
580.667110527329-0.6031723110640.09499505260020.572575363831-0.04166530255970.04213027616720.132207735366-0.366558893417-0.3809601296670.162189386983-0.152881885820.11528134823-0.06544105403930.0921842188142-0.03424932959770.618636268008-0.279967176341-0.01471277131460.7188683774320.1435415678860.475719992849-14.0684333234-32.2986475678-34.5037652349
590.005886867533050.0040660717822-0.01041507036390.00919719115947-0.01408034167640.02019485916140.07499002905280.1271917108760.0359963721934-0.0268584050087-0.133124448191-0.127373162547-0.0183687931236-0.0233262610686-3.00755776125E-51.048112217170.0558096588591-0.3336679387911.08977003994-0.564365149451.36965208478-11.6400092013-43.500104597-50.1619136196
600.0538364272114-0.2109399461180.03231524418430.833438551421-0.09756941612450.06061000752930.1271781015450.020167293138-0.223120433548-0.376480852052-0.195979195521-0.5595728208470.01172163214140.459054796794-0.03254482641350.421046492473-0.128156053088-0.003724087805590.6774812386720.1830691200030.636531873163-5.89464945431-30.9659809391-40.06246408
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 41 )AA4 - 411 - 38
22chain 'A' and (resid 42 through 109 )AA42 - 10939 - 106
33chain 'A' and (resid 110 through 211 )AA110 - 211107 - 208
44chain 'A' and (resid 212 through 237 )AA212 - 237209 - 240
55chain 'B' and (resid 4 through 41 )BC4 - 411 - 38
66chain 'B' and (resid 42 through 140 )BC42 - 14039 - 137
77chain 'B' and (resid 141 through 217 )BC141 - 217138 - 214
88chain 'B' and (resid 218 through 237 )BC218 - 237215 - 240
99chain 'C' and (resid 4 through 41 )CE4 - 411 - 38
1010chain 'C' and (resid 42 through 117 )CE42 - 11739 - 114
1111chain 'C' and (resid 118 through 206 )CE118 - 206115 - 203
1212chain 'C' and (resid 207 through 233 )CE207 - 233204 - 230
1313chain 'C' and (resid 234 through 235 )CE234 - 235231 - 238
1414chain 'D' and (resid 1 through 34 )DG1 - 341 - 34
1515chain 'D' and (resid 35 through 109 )DG35 - 10935 - 109
1616chain 'D' and (resid 110 through 140 )DG110 - 140110 - 140
1717chain 'D' and (resid 141 through 235 )DG141 - 235141 - 235
1818chain 'D' and (resid 236 through 236 )DG236236 - 241
1919chain 'E' and (resid 4 through 17 )EI4 - 171 - 14
2020chain 'E' and (resid 18 through 109 )EI18 - 10915 - 106
2121chain 'E' and (resid 110 through 140 )EI110 - 140107 - 137
2222chain 'E' and (resid 141 through 216 )EI141 - 216138 - 213
2323chain 'E' and (resid 217 through 237 )EI217 - 237214 - 240
2424chain 'F' and (resid 1 through 20 )FK1 - 201 - 20
2525chain 'F' and (resid 21 through 76 )FK21 - 7621 - 76
2626chain 'F' and (resid 77 through 117 )FK77 - 11777 - 117
2727chain 'F' and (resid 118 through 165 )FK118 - 165118 - 165
2828chain 'F' and (resid 166 through 186 )FK166 - 186166 - 186
2929chain 'F' and (resid 187 through 206 )FK187 - 206187 - 206
3030chain 'F' and (resid 207 through 216 )FK207 - 216207 - 216
3131chain 'F' and (resid 217 through 237 )FK217 - 237217 - 243
3232chain 'G' and (resid 2 through 41 )GM2 - 411 - 40
3333chain 'G' and (resid 42 through 76 )GM42 - 7641 - 75
3434chain 'G' and (resid 77 through 140 )GM77 - 14076 - 139
3535chain 'G' and (resid 141 through 165 )GM141 - 165140 - 164
3636chain 'G' and (resid 166 through 190 )GM166 - 190165 - 189
3737chain 'G' and (resid 191 through 214 )GM191 - 214190 - 213
3838chain 'G' and (resid 215 through 235 )GM215 - 235214 - 234
3939chain 'G' and (resid 236 through 237 )GM236 - 237235 - 242
4040chain 'H' and (resid 4 through 34 )HO4 - 341 - 31
4141chain 'H' and (resid 35 through 76 )HO35 - 7632 - 73
4242chain 'H' and (resid 77 through 117 )HO77 - 11774 - 114
4343chain 'H' and (resid 118 through 165 )HO118 - 165115 - 162
4444chain 'H' and (resid 166 through 190 )HO166 - 190163 - 187
4545chain 'H' and (resid 191 through 208 )HO191 - 208188 - 205
4646chain 'H' and (resid 209 through 237 )HO209 - 237206 - 233
4747chain 'I' and (resid 4 through 34 )IQ4 - 341 - 31
4848chain 'I' and (resid 35 through 76 )IQ35 - 7632 - 73
4949chain 'I' and (resid 77 through 140 )IQ77 - 14074 - 137
5050chain 'I' and (resid 141 through 165 )IQ141 - 165138 - 162
5151chain 'I' and (resid 166 through 186 )IQ166 - 186163 - 183
5252chain 'I' and (resid 187 through 214 )IQ187 - 214184 - 211
5353chain 'I' and (resid 215 through 235 )IQ215 - 235212 - 232
5454chain 'I' and (resid 236 through 237 )IQ236 - 237233 - 240
5555chain 'J' and (resid 4 through 76 )JS4 - 761 - 73
5656chain 'J' and (resid 77 through 117 )JS77 - 11774 - 114
5757chain 'J' and (resid 118 through 165 )JS118 - 165115 - 162
5858chain 'J' and (resid 166 through 206 )JS166 - 206163 - 203
5959chain 'J' and (resid 207 through 214 )JS207 - 214204 - 211
6060chain 'J' and (resid 215 through 237 )JS215 - 237212 - 240

+
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