[English] 日本語
Yorodumi
- PDB-8ay7: X-RAY CRYSTAL STRUCTURE OF THE CsPYL1(V112L, T135L,F137I, T153I, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ay7
TitleX-RAY CRYSTAL STRUCTURE OF THE CsPYL1(V112L, T135L,F137I, T153I, V168A)-iSB7-HAB1 TERNARY COMPLEX
Components
  • Abscisic acid receptor PYL1
  • Protein phosphatase 2C 16
KeywordsPLANT PROTEIN / CsPYL1_5M / HAB1 / Phosphatase ABA receptor inhibitor complex
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / protein serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / signaling receptor activity / nucleus / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / Protein phosphatase 2C / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily ...PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / Protein phosphatase 2C / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / : / START-like domain superfamily
Similarity search - Domain/homology
: / Chem-S5N / Abscisic acid receptor PYL1 / Protein phosphatase 2C 16
Similarity search - Component
Biological speciesCitrus sinensis (sweet orange)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.131 Å
AuthorsInfantes, L. / Albert, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: Sci Adv / Year: 2023
Title: Structure-guided engineering of a receptor-agonist pair for inducible activation of the ABA adaptive response to drought.
Authors: Lozano-Juste, J. / Infantes, L. / Garcia-Maquilon, I. / Ruiz-Partida, R. / Merilo, E. / Benavente, J.L. / Velazquez-Campoy, A. / Coego, A. / Bono, M. / Forment, J. / Pampin, B. / Destito, P. ...Authors: Lozano-Juste, J. / Infantes, L. / Garcia-Maquilon, I. / Ruiz-Partida, R. / Merilo, E. / Benavente, J.L. / Velazquez-Campoy, A. / Coego, A. / Bono, M. / Forment, J. / Pampin, B. / Destito, P. / Monteiro, A. / Rodriguez, R. / Cruces, J. / Rodriguez, P.L. / Albert, A.
History
DepositionSep 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Feb 28, 2024Group: Structure summary / Category: entity / Item: _entity.pdbx_description

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Abscisic acid receptor PYL1
B: Protein phosphatase 2C 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,40716
Polymers60,2992
Non-polymers1,10814
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.821, 62.724, 186.948
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Abscisic acid receptor PYL1


Mass: 23269.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrus sinensis (sweet orange) / Gene: CISIN_1g046151mg / Production host: Escherichia coli (E. coli) / References: UniProt: A0A067E666
#2: Protein Protein phosphatase 2C 16 / AtPP2C16 / AtP2C-HA / Protein HYPERSENSITIVE TO ABA 1 / Protein phosphatase 2C HAB1 / PP2C HAB1


Mass: 37029.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HAB1, P2C-HA, At1g72770, F28P22.4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase

-
Non-polymers , 5 types, 92 molecules

#3: Chemical ChemComp-S5N / N-((1,4-dimethyl-2-oxo-1,2-dihydroquinolin-6-yl)methyl)benzenesulfonamide / ~{N}-[(1,4-dimethyl-2-oxidanylidene-quinolin-6-yl)methyl]benzenesulfonamide;


Mass: 342.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.92 %
Crystal growTemperature: 291 K / Method: microbatch / Details: 30% PEG3350 0.5M CaCl2 Drop 1:1 / PH range: 6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.131→44.21 Å / Num. obs: 28817 / % possible obs: 98.91 % / Redundancy: 5.9 % / Biso Wilson estimate: 46.85 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1141 / Rrim(I) all: 0.1255 / Net I/σ(I): 7.37
Reflection shellResolution: 2.131→2.207 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.306 / Mean I/σ(I) obs: 0.92 / Num. unique obs: 2638 / CC1/2: 0.695 / CC star: 0.906 / Rrim(I) all: 1.443 / % possible all: 92.98

-
Processing

Software
NameVersionClassification
XDS2019data reduction
XDS2019data scaling
PHENIX1.19.2-4158phasing
PHENIX1.19.2-4158refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5mn0

5mn0


Resolution: 2.131→44.21 Å / SU ML: 0.2965 / Cross valid method: FREE R-VALUE / σ(F): 0.63 / Phase error: 29.0721
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2473 2649 4.96 %
Rwork0.1909 50759 -
obs0.1938 28817 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.68 Å2
Refinement stepCycle: LAST / Resolution: 2.131→44.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3802 0 57 78 3937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823917
X-RAY DIFFRACTIONf_angle_d0.94445293
X-RAY DIFFRACTIONf_chiral_restr0.0561591
X-RAY DIFFRACTIONf_plane_restr0.0055706
X-RAY DIFFRACTIONf_dihedral_angle_d24.17321456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.131-2.170.34061440.31162323X-RAY DIFFRACTION84.86
2.17-2.210.35421200.29152656X-RAY DIFFRACTION99.07
2.21-2.260.37841490.28772744X-RAY DIFFRACTION99.18
2.26-2.30.30061380.27162672X-RAY DIFFRACTION99.12
2.3-2.360.33181850.25992651X-RAY DIFFRACTION98.85
2.36-2.420.3731510.26022669X-RAY DIFFRACTION98.26
2.42-2.480.30681280.25472668X-RAY DIFFRACTION99.29
2.48-2.560.25411080.23782745X-RAY DIFFRACTION99.51
2.56-2.640.2965920.2362784X-RAY DIFFRACTION99.62
2.64-2.730.32281590.22462688X-RAY DIFFRACTION99.44
2.73-2.840.3411240.22332743X-RAY DIFFRACTION99.51
2.84-2.970.27751330.22082683X-RAY DIFFRACTION99.33
2.97-3.130.29691650.1932683X-RAY DIFFRACTION98.38
3.13-3.320.28731480.19212688X-RAY DIFFRACTION98.64
3.32-3.580.21911530.1712667X-RAY DIFFRACTION98.74
3.58-3.940.20661440.162675X-RAY DIFFRACTION98.88
3.94-4.510.19861300.15832657X-RAY DIFFRACTION97.35
4.51-5.680.20661350.16252662X-RAY DIFFRACTION97.69
5.68-44.210.2221430.17532701X-RAY DIFFRACTION99.16
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.24899949545-2.378405586370.7304696489177.07610153496-1.285717445042.034037718730.15454768551-0.809437611727-0.1055500695920.7697351706590.0726259115175-0.3407459646470.495347398777-0.0938516847692-0.1636150211880.7937404562090.0721770701385-0.1457628726460.7243149687610.03469982986080.5013761590868.675729871637.448982976255.1851565943
22.72781569569-0.163671279575-0.2930387586532.28690691707-0.4526988689052.22783372098-0.00948338755305-0.126168767952-0.2534269156370.1188281981-0.0761592561984-0.2969023598740.3639233196910.520325821580.07382136385990.7148518940930.0856091570799-0.06275603082030.6194351510670.06759605378660.4683690162239.335253710724.5209917277544.8743765259
33.59850107479-0.954300489004-2.497605412281.653551158941.20445049137.49071584405-0.0689110939203-0.0306185723046-0.3440005743120.3320437383430.0425051025470.3609128517161.03792170096-0.6073583766760.03794657905220.519933885738-0.0858380677662-0.01582288487580.4342600642090.03764913070550.402337424532-7.094230824981.9332398342138.2838347527
42.162914415232.91243906471-1.070713983499.255895561620.7694413550776.79353323035-0.1320200576380.493277768037-0.5889553863650.2209263624180.278286674323-0.436391539108-0.0139633706713-0.197118659229-0.1510790354430.4664760140990.0012993853009-0.06210521967160.475499220365-0.02774539279340.4545155674846.905475016670.9050808674529.8439278928
55.820525297460.878340025453-0.4536361754192.758186434470.196543744095.914177020710.211771067477-0.2286410277790.2557056093680.591758063385-0.2696043369790.060872601320.172639413312-0.5097099092690.1695966271710.600494971413-0.0383974986194-0.01527152885920.3776753482360.07726781038720.3760473786892.729602367948.2424901300547.0234904752
62.65648440803-2.82518977205-7.22181633184.266555691852.30634221077.300774217520.738528545504-0.6043426538220.714228381225-0.253694173189-0.0478919556244-0.216821076198-0.08313981670040.525937138758-0.731586293480.582019911328-0.0090452904828-0.03432506872960.43108185876-0.0134105220080.330113224082.219964994213.64961791239.4235752722
72.074746990691.6173243418-3.6489104952.00949806732-3.033273303892.070077768230.162935665647-0.209098488791.097741815320.22141170054-0.1873459037490.641719433326-0.4400977816730.6183651178940.1058422828980.6038451021520.0442384028801-0.138628683730.443596539234-0.05042980802350.501574489549-7.3531714401132.9861886025-4.66244250337
81.277658471451.45171662-1.421156355032.080388584021.982135921562.06545480070.292372462518-0.332214657741-0.27169195748-0.430469248652-0.509262826652-0.3493545370880.9809701340570.9058286301620.3463076817590.3148084157150.0389741494411-0.06323303082480.4280141538960.05975970851990.354809355155-5.6125982961112.60545977247.8487675733
94.07479393345-3.84799300441.219566653032.20755311725-4.691318821017.01327704577-0.2588983475840.07919555157960.1199015810980.107923454604-0.242548421572-0.1426462995090.2681372792280.03455201432230.3237512690820.3228618995610.01209913804450.03314425789130.466561035552-0.0532112789960.399701207102-8.5329311907321.511242006910.0746866484
109.906065714568.677854268631.59250881122.067488059762.148997370248.41051284847-0.108332714157-0.1271826038511.839095723631.229433470931.033756637650.363127331151-1.125381522230.449538698025-1.094229501610.7873043670030.1857408931970.02964069855380.491364417603-0.1228258677770.756417670372-10.356107076741.05106860724.51159513351
112.04384026658-8.65693819698-6.145233713632.023179137272.02804756081.99780179035-0.7558543902180.666600136966-0.7230691054212.04895282656-0.4088407645551.145047200241.37633661349-1.533829624291.36526692540.876010410052-0.03430553991730.2321031385460.603978868785-0.1211725639390.756378430711-1.2544236417349.91797911835.0567547308
123.847505623451.95508928594-3.237977800890.948825588331-1.611346724322.596189494481.31501885815-0.2774627453580.09100369763162.1192045291-1.090215462591.36633307587-0.2441779015060.983505481499-0.2442937677671.10985607547-0.1378242806390.2219113170250.921638315265-0.2873304121611.267563665921.7422653061256.3678484362-2.28123861255
136.13851424546-0.2580426491751.675026023022.85401190688-2.293402420474.97796749880.2377563667460.4100482214691.448597725590.3271024591110.3690566438081.58239945134-1.31146522867-0.813296753606-0.5427076773220.5022138489370.1635832661290.0305769575520.7326488076350.2212557523820.690053301466-7.4399544679343.26983563421.34061974357
143.909744895430.83392274191-0.5616997006197.21943233329-6.695138056532.39009958738-0.182617215922-0.415279429116-0.1884540171-0.4115291907780.3503470222940.2025605086570.564153764829-0.826359082521-0.2070052011450.435445161866-3.43572341538E-50.005752848554180.323310568220.006649158859180.25268652104-5.1047899422423.550440271313.7042399984
153.719406675262.51044618374-1.11978019812.11793518244-3.703209333737.645099489460.425415310949-0.4684053073430.6819144744640.249979545544-0.4091033181470.639436624481-0.9618194547920.0385211995441-0.03308032288060.4466267695230.001490540478220.04441896784750.50107008511-0.07105191544070.455094093022-9.9767420929636.723880527715.8902832258
1610.23155990826.11529562294-6.011375176793.51600074733-6.211147789083.242386146280.2977820968460.234926294956-0.1516831530650.9654129111260.0907949723994-0.66181714897-0.8686353673040.0337778288872-0.3834340577910.7078268791790.01466093456580.009888287039280.563080097973-0.180029530280.566047531547-1.0253147762738.637292588618.4152878904
172.25872482314-2.25405588922-4.245973441212.05150419987-0.3681275603352.0203827444.05816895809E-5-0.94507333164-0.3509676373160.502721751002-0.0374771959824-0.1265094087490.58536367134-2.23089510635-0.04200010332810.9299648679170.0505185800328-0.05700975393130.9977707885930.144223337170.655636086641-12.721479086332.714506375628.0985129032
182.06886210183-2.545766162931.699537174456.33032537677-2.808762537072.69486498898-0.0452561706297-0.6146784290790.04124531645320.6127259433720.5937257735761.42541936165-0.43690892973-0.402961017395-0.4646124739680.602818004456-0.0284513048350.06258691417160.4559954094990.03135157593640.612472001844-6.6293860666829.287119428318.7744132376
192.10211219476-1.152125326130.049780550421.76620013513-0.4558914659523.49018480461-0.0152114532556-0.4145766503660.1566987219720.1746177283410.0363097557658-0.1692071381690.2580219762440.246489306026-0.000200154340190.424921013242-0.08997761773320.005006820426410.456390406168-0.03675532396170.3769971871198.4928164428928.81105580567.8096987657
208.79544342666-5.80956679472-2.223154583182.24507414099-0.5869696984582.10709566982-0.23482937092-0.2246638684070.6347391656150.103200089158-0.229380893682-1.16804635285-0.8410387293711.933563311760.4972849111830.587053327999-0.128196501196-0.03810955408150.601399964620.08489257756250.58357985310815.358286460527.516607567126.5905368475
219.31987512107-0.686123461444-0.03757065104552.262540033812.924941577433.586492017360.161388766563-0.141213637821-0.3038490506150.6172838424750.00497918828691-0.7425281927580.580588139090.835538678199-0.1669124477930.477950818970.0909327371673-0.02289058258310.6111046925130.08000168816240.37214829805211.78652819915.668699135327.7053184083
221.07063134106-1.233531429340.3206843060091.41174830126-0.3497792102190.0987637419330.0667848076935-0.0981696441549-0.1265193090360.212289154241-0.0943784144380.0825695680301-0.611385827274-0.1796598151040.0561688732570.549504317423-0.007298438651450.0005252615583880.5266185418940.05306421175710.3525406746233.6000010747322.987680323123.2138519635
235.57663651784-2.168010224631.919708932845.47658498813-3.770945480862.18068363688-0.50715424996-1.022232970150.4342552180350.3590893612560.473042335160.1705830569630.674577279845-0.797980822427-0.0311246503490.65262265404-0.0111206013342-0.03309576554560.559945002863-0.08898185578430.3585087549042.746589817227.296707438528.2379000413
245.983520116311.5592478336-3.381746222225.593355736581.207640822.09202082680.315022666689-0.08254052330740.68425425972-0.334657159246-0.0477385486289-0.335042431319-1.115948051861.31633692036-0.16780067560.400564821427-0.03851155047920.02585398523060.4239346502790.01369163193650.5329029510337.1267683837538.35084534871.73282591761
250.932662969888-1.475523410910.3677103579857.83687940135-5.685947703596.309769145450.149298611883-0.009430002794070.0482843522228-0.168984835076-0.387531651979-0.1556656688740.02320388615410.7077068888920.2289305935030.245416230721-0.0457481362317-0.02434604856850.457885002384-0.02253185937580.3728966926665.2183395541121.80916514542.96798538561
263.49278168835-0.003840772573964.796635216922.291690455350.4374321138773.063962373390.1697545054610.402891815991-0.71089720388-0.28478587180.112849018379-0.09348080449910.4160707704480.211100992002-0.2024977572880.39684996905-0.001859883829930.02659592745090.427627199789-0.01997383769660.3209298925223.2998435062721.3504154432-10.2003137371
271.10930629859-0.181670931744-0.9414802155812.38560230743-1.060511224088.133660997840.2702914657040.5543101961460.1516247753-0.84631013175-0.348897296731.04105931335-1.43572364167-0.106648788449-0.04185720052160.686016196897-0.0163861273274-0.09863374462970.571058503844-0.01371829209420.578026153795-11.752463100929.911367824-11.267737561
285.85364266753-6.63714680045.901710472282.48930608392-9.3158247304110.15814156570.5872823734970.0399501114483-0.824922029221-1.16826574892-0.04925297246510.8826301860591.09146826552-0.522272731605-0.5077734188840.393755543151-0.0800644513524-0.03019661359190.357285125449-0.03360000864450.408902917678-1.5809489159115.3975940427-3.61743493391
294.265056889850.351507549609-3.17077449675.453960182420.614514542632.80489550517-0.04181086942480.2518736140790.216048393385-0.2690090508470.4368868921680.253564532654-0.121917748795-0.511826391044-0.3856015528210.235622181573-0.0519867629421-0.0890920153430.3972668862040.001173087398970.327529967150.22734873572621.9290333445-0.585943802664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 141 )
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 149 )
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 181 )
6X-RAY DIFFRACTION6chain 'A' and (resid 182 through 207 )
7X-RAY DIFFRACTION7chain 'B' and (resid 186 through 190 )
8X-RAY DIFFRACTION8chain 'B' and (resid 191 through 200 )
9X-RAY DIFFRACTION9chain 'B' and (resid 201 through 210 )
10X-RAY DIFFRACTION10chain 'B' and (resid 211 through 215 )
11X-RAY DIFFRACTION11chain 'B' and (resid 216 through 221 )
12X-RAY DIFFRACTION12chain 'B' and (resid 222 through 232 )
13X-RAY DIFFRACTION13chain 'B' and (resid 233 through 237 )
14X-RAY DIFFRACTION14chain 'B' and (resid 238 through 248 )
15X-RAY DIFFRACTION15chain 'B' and (resid 249 through 273 )
16X-RAY DIFFRACTION16chain 'B' and (resid 281 through 302 )
17X-RAY DIFFRACTION17chain 'B' and (resid 303 through 308 )
18X-RAY DIFFRACTION18chain 'B' and (resid 315 through 337 )
19X-RAY DIFFRACTION19chain 'B' and (resid 338 through 368 )
20X-RAY DIFFRACTION20chain 'B' and (resid 369 through 378 )
21X-RAY DIFFRACTION21chain 'B' and (resid 379 through 392 )
22X-RAY DIFFRACTION22chain 'B' and (resid 393 through 402 )
23X-RAY DIFFRACTION23chain 'B' and (resid 403 through 413 )
24X-RAY DIFFRACTION24chain 'B' and (resid 414 through 423 )
25X-RAY DIFFRACTION25chain 'B' and (resid 424 through 439 )
26X-RAY DIFFRACTION26chain 'B' and (resid 440 through 458 )
27X-RAY DIFFRACTION27chain 'B' and (resid 459 through 471 )
28X-RAY DIFFRACTION28chain 'B' and (resid 472 through 487 )
29X-RAY DIFFRACTION29chain 'B' and (resid 488 through 505 )

+
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