[English] 日本語
Yorodumi
- PDB-7tvj: Crystal Structure of Monobody Mb(SHP2PTP_13)/SHP2 PTP Domain Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tvj
TitleCrystal Structure of Monobody Mb(SHP2PTP_13)/SHP2 PTP Domain Complex
Components
  • Mb(SHP2PTP_13)
  • Tyrosine-protein phosphatase non-receptor type 11
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / Monobody / SHP2 / Phosphatase / Complex / Inhibitor / Signaling / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Co-inhibition by BTLA / Netrin mediated repulsion signals ...negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Co-inhibition by BTLA / Netrin mediated repulsion signals / negative regulation of neutrophil activation / cerebellar cortex formation / positive regulation of hormone secretion / regulation of protein export from nucleus / Interleukin-37 signaling / positive regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of ossification / Signaling by Leptin / MET activates PTPN11 / hormone metabolic process / Regulation of RUNX1 Expression and Activity / negative regulation of chondrocyte differentiation / Signal regulatory protein family interactions / face morphogenesis / ERBB signaling pathway / platelet formation / triglyceride metabolic process / organ growth / megakaryocyte development / Interleukin-20 family signaling / negative regulation of type I interferon production / Interleukin-6 signaling / PI-3K cascade:FGFR3 / Co-inhibition by CTLA4 / Platelet sensitization by LDL / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / peptide hormone receptor binding / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / MAPK3 (ERK1) activation / Prolactin receptor signaling / neurotrophin TRK receptor signaling pathway / regulation of cell adhesion mediated by integrin / regulation of type I interferon-mediated signaling pathway / MAPK1 (ERK2) activation / platelet-derived growth factor receptor signaling pathway / PECAM1 interactions / Bergmann glial cell differentiation / inner ear development / peptidyl-tyrosine dephosphorylation / non-membrane spanning protein tyrosine phosphatase activity / phosphoprotein phosphatase activity / positive regulation of intracellular signal transduction / Regulation of IFNA/IFNB signaling / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / Co-inhibition by PD-1 / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / positive regulation of insulin receptor signaling pathway / ephrin receptor signaling pathway / regulation of protein-containing complex assembly / Regulation of IFNG signaling / Activated NTRK2 signals through FRS2 and FRS3 / GPVI-mediated activation cascade / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / cell adhesion molecule binding / negative regulation of T cell proliferation / T cell costimulation / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / hormone-mediated signaling pathway / FRS-mediated FGFR1 signaling / Tie2 Signaling / phosphotyrosine residue binding / protein-tyrosine-phosphatase / FLT3 Signaling / Downstream signal transduction / homeostasis of number of cells within a tissue / positive regulation of mitotic cell cycle / axonogenesis / protein tyrosine phosphatase activity / positive regulation of interferon-beta production / protein tyrosine kinase binding / cellular response to epidermal growth factor stimulus / DNA damage checkpoint signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / integrin-mediated signaling pathway / positive regulation of D-glucose import across plasma membrane / insulin receptor binding / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / cellular response to mechanical stimulus / Spry regulation of FGF signaling
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-6, -11 / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. ...Protein-tyrosine phosphatase, non-receptor type-6, -11 / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Tyrosine-protein phosphatase non-receptor type 11
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsSha, F. / Koide, S.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM072688 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01DA048764 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM090324 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008720-S United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5P41RR015301-10 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)8 P41 GM103403-10 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: J.Mol.Biol. / Year: 2023
Title: Monobody Inhibitor Selective to the Phosphatase Domain of SHP2 and its Use as a Probe for Quantifying SHP2 Allosteric Regulation.
Authors: Sha, F. / Kurosawa, K. / Glasser, E. / Ketavarapu, G. / Albazzaz, S. / Koide, A. / Koide, S.
History
DepositionFeb 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Mar 15, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 11
B: Mb(SHP2PTP_13)
D: Tyrosine-protein phosphatase non-receptor type 11
E: Mb(SHP2PTP_13)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1606
Polymers90,7824
Non-polymers3782
Water4,035224
1
A: Tyrosine-protein phosphatase non-receptor type 11
B: Mb(SHP2PTP_13)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5803
Polymers45,3912
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-4 kcal/mol
Surface area15920 Å2
MethodPISA
2
D: Tyrosine-protein phosphatase non-receptor type 11
E: Mb(SHP2PTP_13)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5803
Polymers45,3912
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-5 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.460, 48.490, 102.070
Angle α, β, γ (deg.)80.140, 77.530, 61.630
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 11 / Protein-tyrosine phosphatase 1D / PTP-1D / Protein-tyrosine phosphatase 2C / PTP-2C / SH-PTP2 / SHP- ...Protein-tyrosine phosphatase 1D / PTP-1D / Protein-tyrosine phosphatase 2C / PTP-2C / SH-PTP2 / SHP-2 / Shp2 / SH-PTP3


Mass: 35292.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PTP domain (UNP residues 224-525) / Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11, PTP2C, SHPTP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06124, protein-tyrosine-phosphatase
#2: Protein Mb(SHP2PTP_13)


Mass: 10098.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 5
Details: 0.1 M sodium citrate tribasic dihydrate, 2% Tascimate, 16% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.39→49.67 Å / Num. obs: 29422 / % possible obs: 93.3 % / Redundancy: 1.8 % / Biso Wilson estimate: 25.39 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.084 / Rrim(I) all: 0.118 / Net I/σ(I): 6.7
Reflection shellResolution: 2.39→2.48 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3038 / CC1/2: 0.531 / Rpim(I) all: 0.245 / Rrim(I) all: 0.347 / % possible all: 92.1

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3ZM1 & 3K2M

3zm1

3k2m


Resolution: 2.39→49.67 Å / SU ML: 0.2961 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 25.4513
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2588 1473 5.09 %
Rwork0.2291 27471 -
obs0.2306 28944 91.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.15 Å2
Refinement stepCycle: LAST / Resolution: 2.39→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5491 0 26 224 5741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215713
X-RAY DIFFRACTIONf_angle_d0.53487791
X-RAY DIFFRACTIONf_chiral_restr0.0452867
X-RAY DIFFRACTIONf_plane_restr0.0033999
X-RAY DIFFRACTIONf_dihedral_angle_d5.355801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.470.30621120.26982049X-RAY DIFFRACTION75.4
2.47-2.560.30881190.26942632X-RAY DIFFRACTION94.83
2.56-2.660.26061530.25752496X-RAY DIFFRACTION93.8
2.66-2.780.27951460.26212570X-RAY DIFFRACTION94.14
2.78-2.930.321250.25962546X-RAY DIFFRACTION93.72
2.93-3.110.27271310.24662529X-RAY DIFFRACTION92.59
3.11-3.350.27391360.23552456X-RAY DIFFRACTION91.59
3.35-3.690.24591360.22212447X-RAY DIFFRACTION89.5
3.69-4.220.24541420.2012593X-RAY DIFFRACTION95.66
4.22-5.310.23131340.19242603X-RAY DIFFRACTION95.07
5.31-49.670.22891390.22452550X-RAY DIFFRACTION93.96
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)
12.395179386310.968549480961-0.4501504962442.977358003450.1523645515822.408061191340.16580022856-0.1942459458460.00409585682790.599085988817-0.04956458034860.620529229860.174732504357-0.0886106669543-0.0834080005610.237209454986-0.02933172390770.09094364243350.1622089461420.03680790547850.25988953965319.8084586091-1.0253535006229.5136945689
21.557100375330.498559496206-0.5508145549533.602828535790.489032106542.947284612590.0761070901460.0579187229731-0.144294515923-0.1575717443470.08791368357130.6390567029720.2583671549340.0412731583466-0.1551185888980.159063170164-0.0389512417603-0.05794653276820.1473321219410.054628727360.26986441992323.5196723922-8.16139594919.3862231753
33.201986285170.2102042028450.2505249624732.676030136130.09636430146853.206796250080.154129020901-0.2211410588717.15422665106E-5-0.5159691214050.0124357185242-0.5070484785630.4745422822270.0617673272688-0.1664189653120.3377862271670.0714352786987-0.001127500023360.151592375358-0.03039073253460.28190839111836.620426502-10.302647554313.2461069971
42.868214634741.393905663730.5177295786624.954543174323.974510028426.06941027916-0.2316734415920.1469881149730.202112353975-0.1008740785020.318653071161-0.314094424804-0.3609015508290.747118123029-0.1409102775750.192173647402-0.0239995745124-0.02239517884150.1619615404610.02201410546360.31086137364438.8213510146.6611912782513.1882197445
52.15914382606-0.0388493433666-1.080000846763.08554288741.178740337340.965766245570.0534510101666-0.1516571270630.096799894771-0.318709016608-0.1562689239080.0668467328019-0.214032717476-0.0278647601082-0.05126963218250.227768003975-0.00536488764389-0.002936862522620.108473044832-0.006633739730910.23155886977528.83754126095.2784826391312.9896472113
62.195379728160.759183514873-0.4174824353842.96578317516-2.10921475832.078244181580.0568497229563-0.1309320432960.3589472299890.1520544344860.0501232689612-0.124192851643-0.494181631371-0.0362583869558-0.1187013574250.348944063343-0.002801085815230.02224357539240.10640841796-0.05304346581840.26170887292528.800307101915.451663026918.3426016407
75.351921031871.34575237323-0.1863062607492.503595411811.023736080653.668489339240.549378712584-0.573354683857-0.0140701663609-0.00307966525119-0.159413969887-0.1395857779340.594642085438-0.131908046069-0.2974751568390.41614257767-0.05249701203720.0456056908360.4621667871660.03101586803840.12686115835724.66023725882.6521729632246.0269068715
81.410343839010.4604167110660.7864638528822.30119852160.2778087861410.43873369995-0.0341995632652-0.01820858643360.02301934341440.9380828084210.0703035331792-0.506298325004-0.1725228003060.473611798481-0.2149479450420.559079814541-0.147067555696-0.0949179123111.00223635371-0.111419444710.29133235996939.71562930999.9678181141155.0039766706
91.96244711239-0.968922808084-0.2408621756711.05247149216-0.5860003079690.895216554078-0.157880302726-0.2226517082820.5065986595660.177172440624-0.180248853286-0.0241173405167-0.110983531644-0.08993342492250.07659478401830.729809467794-0.587206500152-0.2031451323760.96302965165-0.1071254895720.58434091666242.105644614713.983866999251.5107640106
104.71155908596-0.270474359052.484228420785.94145708107-3.723334605289.16438365663-0.02591595277570.2603914311670.008895014782660.03232655695610.366870179244-0.3405933427380.3344437585570.705225901584-0.1437737295730.3149596483430.0358943247695-0.04236461829740.4421595719730.01183476396950.19095871197830.47045128810.84734091787339.603454551
114.428802951630.303877978805-0.1680797453313.32924892339-1.677572187780.8458870950410.205721932004-0.4281277602340.7485522476740.48852099392-0.11662876464-0.0630036570383-0.3396845000180.105870724694-0.01101565024610.610418482859-0.4157681768310.05675331054610.698654321269-0.06460054228490.51320899601633.342633213415.670119632942.5077917523
120.317097003069-0.223160720872-0.4034687210680.1525361454010.2785904419870.7728055126160.1465099609710.151744162190.2821490846550.0759236616280.268725863440.285440803042-0.344070270322-0.196048028314-0.6681136186140.720437604515-0.4264542074540.06688051117280.7017324369840.1838347603840.32178562228235.139315202318.924967781743.4700637829
131.662783916770.467432721854-0.1382247057991.551916736720.9598766337651.906711043150.05451246840520.04914521308950.1776537604010.118121083508-0.399905132399-0.139410853929-0.4218149748930.3834088008640.3239416971880.451068239286-0.389698501071-0.1653425504611.330560991460.1520955104960.37457598392540.91501727613.439832684345.8367605921
144.180143738233.922021312395.423962137965.73287990485.980144184657.431387887820.247621514036-0.5847869641850.2380817923270.209919236118-0.3010131271220.195837686104-0.407225205524-0.04241427997710.1546491985740.500949494281-0.144689015735-0.01728913806430.362396035241-0.01774597049820.066557008332425.77736382710.955168392242.4195330943
154.238472799-0.005895363477342.115669708571.932008312460.2220229269522.71127609205-0.2142089331-0.5857701513420.3024642833850.5625377118740.144526805471-0.217183392343-0.3860471816390.5102924081490.01949732576570.892835114553-0.316282871534-0.03333254108540.511746600539-0.05562775554250.19754977268932.273925094514.771006128354.958929841
165.06618048118-1.627110085910.5923783832681.20193779208-0.1101243968543.709525808610.2497499478470.3971138467690.536256531559-0.0979573498072-0.214409227618-0.319085534453-0.1831752703330.172798105929-0.03406692697720.20811079826-0.002587098594710.05711043678250.1469298305460.05278476583320.25727607050431.79586576566.4927050119570.0367434571
172.95711116055-0.007464365468131.453221115781.71075139656-1.43064926151.89885374734-0.1681668427060.3962821293050.1492837808570.05018199895540.03303178205760.0476098393038-0.2355171665420.1599928149870.01290690584450.1140277791140.00565914356041-0.01584911577470.314813917925-0.001629075810710.27390668197937.2230100764.089480841978.2387500913
183.09499761378-0.7449613996540.1954055442193.65702471777-0.6330386163782.92994855309-0.0488814491767-0.112542322415-0.254245570178-0.1265198446870.0919715954432-0.06925941672510.1956316535660.00735915980565-0.07476773626410.1453294068280.05912385271140.02284426019810.169726428086-0.0008827099962150.24723382913532.1949815183-10.574958690583.9345320399
192.01262979358-0.5125585170460.1086147562892.42767846976-0.9002029213022.3193986306-0.0596500933716-0.472910053036-0.3022806519270.09013461203610.14089021894-0.3920670470660.219194316770.645206002823-0.0109786474850.170070214760.09005806298520.03078336079770.315888901209-0.0501733534310.27340995923635.4596185569-9.4168721696391.5189787819
204.44261373756-0.1129160371651.437654117062.02723068634-1.116069631113.77405925887-0.00771400749634-0.490350857108-0.1356027720580.09968281975770.1023995157010.08023584250380.0788407337281-0.371687040926-0.1115993091550.1528128817480.06808759891830.01533440711440.147997463616-0.01707357044140.20802683177419.9725759301-4.9003085134685.889104482
212.05080870335-0.0429534907584-0.9696063715213.094127057010.09936522682311.83803456505-0.113442289746-0.1589370285910.2250739961010.1609697118440.2407782635390.318923621218-0.2768785928130.0673616883609-0.07102164886630.1451855622880.0602954925796-0.02061467634440.2779504546130.003787512322610.1684242862116.93623087727.2723780981582.8961197287
223.45362938647-0.132587737319-0.6300342442974.84281316851.226877069182.14976400945-0.004703792389360.2051101611880.2037046090010.1507758109360.1024163075070.773478909456-0.03520432949-0.5506236130150.0511508720530.1291713449010.0574399650885-0.01295312029790.2581852578230.01111834315820.3383795753727.721270913371.705171204783.5488165004
231.919344352950.659493101682.28176761511.647626181870.9827998325833.197330337470.0362699184942-0.0588478492482-0.160935170064-0.1936987286250.3614069528660.1165196547720.229327770009-0.1287347555880.1350177337980.432123727332-0.118791749425-0.1357130910330.4644911309290.0361640740870.077515815537420.90350188490.85652579395650.4693142873
244.247699537410.7323843036564.225951825211.293424019460.1845425803715.14056720580.1535806306150.2165916290.150768208433-0.249075599334-0.08863030818730.216337149120.684478211506-0.468339152574-0.2452481597730.264348641911-0.145975108751-0.04450357934730.5643366966380.002665350159270.20799620790716.4407921819-0.15640898715456.6876509935
252.93334587902-0.8609974693632.376309339281.05553680986-0.1284989568913.514232777120.0258502132028-0.145890933606-0.009019081335930.18884119572-0.162807955958-0.0311958972940.134572304927-0.773698026353-0.06569539294330.530414679958-0.4164401624970.01286811200020.8812719637160.05797577357410.2356284950157.87301296983-0.18741920964755.5653896697
263.15740079940.1223972793772.255764180584.633255238390.3438866524895.36819292432-0.4908877651460.3755499110590.751176541068-0.710979673172-0.0001091777530250.2827720573410.131590407421-0.8197467124450.4481093342050.306593977243-0.0450162888594-0.004001202434990.3661058417450.03314934600870.39497071715616.99704842496.9773036319455.9770171231
273.659330673660.2317555598611.104017207710.7209917151990.3492760991420.4432520779190.003686470079681.067871522320.184205438346-0.9914114601450.04925139070510.462460048860.199082217452-0.221354456942-0.04854391833430.588942791359-0.159256479563-0.1679790829850.9575362806640.1825757339610.2552557668810.14443630163.5377194654543.9363842775
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 248 through 296 )AA248 - 2961 - 49
22chain 'A' and (resid 297 through 347 )AA297 - 34750 - 92
33chain 'A' and (resid 348 through 420 )AA348 - 42093 - 165
44chain 'A' and (resid 421 through 447 )AA421 - 447166 - 192
55chain 'A' and (resid 448 through 482 )AA448 - 482193 - 227
66chain 'A' and (resid 483 through 525 )AA483 - 525228 - 270
77chain 'B' and (resid 2 through 10 )BB2 - 101 - 9
88chain 'B' and (resid 11 through 16 )BB11 - 1610 - 15
99chain 'B' and (resid 17 through 25 )BB17 - 2516 - 24
1010chain 'B' and (resid 26 through 34 )BB26 - 3425 - 33
1111chain 'B' and (resid 35 through 41 )BB35 - 4134 - 40
1212chain 'B' and (resid 42 through 55 )BB42 - 5541 - 49
1313chain 'B' and (resid 56 through 72 )BB56 - 7250 - 62
1414chain 'B' and (resid 73 through 88 )BB73 - 8863 - 78
1515chain 'B' and (resid 89 through 93 )BB89 - 9379 - 83
1616chain 'D' and (resid 250 through 296 )DD250 - 2961 - 47
1717chain 'D' and (resid 297 through 322 )DD297 - 32248 - 66
1818chain 'D' and (resid 323 through 405 )DD323 - 40567 - 149
1919chain 'D' and (resid 406 through 420 )DD406 - 420150 - 164
2020chain 'D' and (resid 421 through 463 )DD421 - 463165 - 207
2121chain 'D' and (resid 464 through 507 )DD464 - 507208 - 251
2222chain 'D' and (resid 508 through 525 )DD508 - 525252 - 269
2323chain 'E' and (resid 2 through 21 )EE2 - 211 - 14
2424chain 'E' and (resid 22 through 42 )EE22 - 4215 - 35
2525chain 'E' and (resid 43 through 71 )EE43 - 7136 - 55
2626chain 'E' and (resid 72 through 88 )EE72 - 8856 - 72
2727chain 'E' and (resid 89 through 95 )EE89 - 9573 - 79

+
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