[English] 日本語
Yorodumi
- PDB-7z3t: Crystal structure of apo human Cathepsin L -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7z3t
TitleCrystal structure of apo human Cathepsin L
ComponentsCathepsin L
KeywordsHYDROLASE / cathepsin / cystein protease / drug development / drug target / peptide-like inhibitor / lysosome / protein degradation / SARS-CoV-2 / COVID-19 / spike protein maturation
Function / homology
Function and homology information


enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus ...enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / zymogen activation / Assembly of collagen fibrils and other multimeric structures / antigen processing and presentation / protein autoprocessing / Collagen degradation / collagen catabolic process / fibronectin binding / serpin family protein binding / collagen binding / Attachment and Entry / Degradation of the extracellular matrix / receptor-mediated endocytosis of virus by host cell / multivesicular body / endocytic vesicle lumen / MHC class II antigen presentation / cysteine-type peptidase activity / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / : / histone binding / adaptive immune response / Attachment and Entry / lysosome / apical plasma membrane / fusion of virus membrane with host plasma membrane / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Procathepsin L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsReinke, P.Y.A. / Falke, S. / Lieske, J. / Ewert, W. / Loboda, J. / Rahmani Mashhour, A. / Hauser, M. / Karnicar, K. / Usenik, A. / Lindic, N. ...Reinke, P.Y.A. / Falke, S. / Lieske, J. / Ewert, W. / Loboda, J. / Rahmani Mashhour, A. / Hauser, M. / Karnicar, K. / Usenik, A. / Lindic, N. / Lach, M. / Boehler, H. / Beck, T. / Cox, R. / Chapman, H.N. / Hinrichs, W. / Turk, D. / Guenther, S. / Meents, A.
Funding support Germany, Slovenia, 6items
OrganizationGrant numberCountry
Helmholtz AssociationFISCOV Germany
Helmholtz AssociationSFragX Germany
German Federal Ministry for Education and Research16GW0277 Germany
German Federal Ministry for Education and Research031B0405 Germany
Slovenian Research AgencyP1-0048 Slovenia
Slovenian Research AgencyIO-0048 Slovenia
Citation
Journal: Commun Biol / Year: 2023
Title: Calpeptin is a potent cathepsin inhibitor and drug candidate for SARS-CoV-2 infections.
Authors: Reinke, P.Y.A. / de Souza, E.E. / Gunther, S. / Falke, S. / Lieske, J. / Ewert, W. / Loboda, J. / Herrmann, A. / Rahmani Mashhour, A. / Karnicar, K. / Usenik, A. / Lindic, N. / Sekirnik, A. ...Authors: Reinke, P.Y.A. / de Souza, E.E. / Gunther, S. / Falke, S. / Lieske, J. / Ewert, W. / Loboda, J. / Herrmann, A. / Rahmani Mashhour, A. / Karnicar, K. / Usenik, A. / Lindic, N. / Sekirnik, A. / Botosso, V.F. / Santelli, G.M.M. / Kapronezai, J. / de Araujo, M.V. / Silva-Pereira, T.T. / Filho, A.F.S. / Tavares, M.S. / Florez-Alvarez, L. / de Oliveira, D.B.L. / Durigon, E.L. / Giaretta, P.R. / Heinemann, M.B. / Hauser, M. / Seychell, B. / Bohler, H. / Rut, W. / Drag, M. / Beck, T. / Cox, R. / Chapman, H.N. / Betzel, C. / Brehm, W. / Hinrichs, W. / Ebert, G. / Latham, S.L. / Guimaraes, A.M.S. / Turk, D. / Wrenger, C. / Meents, A.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Adams, P.D. / Afonine, P.V. / Bunkoczi, G. / Chen, V.B. / Davis, I.W. / Echols, N. / Headd, J.J. / Hung, L.W. / Kapral, G.J. / Grosse-Kunstleve, R.W. / McCoy, A.J. / Moriarty, N.W. / ...Authors: Adams, P.D. / Afonine, P.V. / Bunkoczi, G. / Chen, V.B. / Davis, I.W. / Echols, N. / Headd, J.J. / Hung, L.W. / Kapral, G.J. / Grosse-Kunstleve, R.W. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R. / Read, R.J. / Richardson, D.C. / Richardson, J.S. / Terwilliger, T.C. / Zwart, P.H.
History
DepositionMar 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Oct 16, 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: Cathepsin L
B: Cathepsin L
C: Cathepsin L
D: Cathepsin L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,82321
Polymers96,7114
Non-polymers2,11217
Water10,557586
1
A: Cathepsin L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7086
Polymers24,1781
Non-polymers5315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cathepsin L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6905
Polymers24,1781
Non-polymers5134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cathepsin L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7966
Polymers24,1781
Non-polymers6195
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cathepsin L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6284
Polymers24,1781
Non-polymers4513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.940, 62.140, 67.470
Angle α, β, γ (deg.)105.166, 94.226, 115.576
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Cathepsin L


Mass: 24177.676 Da / Num. of mol.: 4 / Mutation: T110A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSL, CTSL1 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P07711

-
Non-polymers , 5 types, 603 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 586 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: Mature cathepsin L at a concentration of 7 mg/ml was equilibrated against 27% w/v PEG 8000, 1 mM TCEP and 0.1 M sodium acetate at pH 4.0. Crystals, which grew at 293 K to final size after approximately 3 days.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.6→49.94 Å / Num. obs: 101082 / % possible obs: 97.22 % / Redundancy: 7.2 % / Biso Wilson estimate: 19.36 Å2 / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.1661 / Rpim(I) all: 0.06553 / Rrim(I) all: 0.1793 / Net I/σ(I): 9.07
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 7.6 % / Rmerge(I) obs: 2.183 / Mean I/σ(I) obs: 2.33 / Num. unique obs: 10076 / CC1/2: 0.55 / CC star: 0.842 / Rpim(I) all: 0.839 / Rrim(I) all: 2.345 / % possible all: 96.66

-
Processing

Software
NameVersionClassification
PHENIX1.18-3855_9999refinement
Cootmodel building
autoPROCdata reduction
XSCALEdata scaling
PHENIX1.18-3855_9999phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QKC

7qkc


Resolution: 1.6→49.94 Å / SU ML: 0.1508 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.1633
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.176 1993 1.97 %
Rwork0.1547 98920 -
obs0.1551 100913 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.23 Å2
Refinement stepCycle: LAST / Resolution: 1.6→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6764 0 140 586 7490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00557400
X-RAY DIFFRACTIONf_angle_d0.79599994
X-RAY DIFFRACTIONf_chiral_restr0.0487976
X-RAY DIFFRACTIONf_plane_restr0.00481341
X-RAY DIFFRACTIONf_dihedral_angle_d12.76411122
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.25041460.2487032X-RAY DIFFRACTION96.62
1.64-1.680.25921410.22317047X-RAY DIFFRACTION96.94
1.68-1.730.20961360.2077049X-RAY DIFFRACTION97.17
1.73-1.790.22771520.20157040X-RAY DIFFRACTION97.29
1.79-1.850.24881450.19647013X-RAY DIFFRACTION97.22
1.85-1.930.20351250.18846841X-RAY DIFFRACTION92.76
1.93-2.020.21011560.16097110X-RAY DIFFRACTION98.32
2.02-2.120.17471430.14957174X-RAY DIFFRACTION98.33
2.12-2.260.16481350.14977152X-RAY DIFFRACTION98.79
2.26-2.430.16711420.1477152X-RAY DIFFRACTION98.55
2.43-2.670.16321400.14696969X-RAY DIFFRACTION95.65
2.67-3.060.17461520.1497217X-RAY DIFFRACTION99.01
3.06-3.860.16631420.13477151X-RAY DIFFRACTION98.7
3.86-49.940.14561380.14196973X-RAY DIFFRACTION95.87
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)
13.023767206220.09789928411711.447085046111.54471064890.4985604642741.87527551557-0.149916588158-0.096484696241-0.00968930438865-0.0747058721030.107929994671-0.133405053412-0.1486985065130.008327658662060.06588970188340.251306423022-0.03609063380450.08386022467940.223065724997-0.07437912063720.20902217068225.91696647-9.18207467944-5.14138963692
25.066633239281.93191016262-2.771565038441.85322484575-2.119429803183.83692055005-0.07018321427760.00664285604702-0.184564393805-0.2836869270070.12000937251-0.362402123716-0.06047206844610.260720138423-0.03475500121840.225178156643-0.0625159833280.07321560123930.203065814377-0.1118429741940.21765391153426.3421040072-16.2403682941-11.8823317112
33.114747867920.9799937789451.390977287142.813922469530.9941240529151.096671000570.006328649573420.01068241366070.161533824279-0.2590144716580.1412738894360.142268417169-0.0935541519278-0.0106557147379-0.1050597488450.244215780086-0.05154958282780.09006755220010.179228439392-0.06792934208910.15344122452619.2703710286-19.4872754833-16.1444747254
42.69653706971-0.1079925414020.7118722371763.225643714630.3627227042213.775583203160.0558074473583-0.0308330892993-0.109100796345-0.2314585758140.0767409921978-0.01951350880470.0480177291482-0.230978377753-0.127490281280.203502696148-0.07251674816360.0422079199750.165227067469-0.05481392760110.17779285156416.7306709586-22.6397956472-15.9818842293
51.077084136960.2810065673621.133728065732.104731867950.7006132142736.024698991380.0364766429362-0.041253968541-0.3247445854280.1201397732850.397977553458-0.5667670556320.1934097873050.184267175517-0.4705585728430.197883954140.0135597893210.02496418864920.229243132927-0.1023450065170.38039173595333.6997305081-21.0351321549-4.32059644308
61.141201664820.8380517134841.440861057281.748854678641.779819401923.42885407610.126474656389-0.279085436507-0.1086509783390.124307940694-0.0287651334301-0.06697977699520.101788329665-0.402207655064-0.08579077685290.168028752519-0.0181524583020.0214719527370.222101238409-0.004626793221340.16281860116524.3366287991-10.96162063347.22988234206
72.85376740328-0.343691284220.692720667352.630397733761.015241088142.636670002370.0184359980396-0.179814427321-0.08687113457920.07634996027110.0967393322065-0.3271238173890.0125989495202-0.0174652538185-0.1107379673350.160273788561-0.06297962736550.03268366296090.150319114106-0.03810677547060.18353866553824.9992631261-12.6324386162.24409121135
84.17513784151-1.05586546531-0.3197318813784.85864043903-0.01104278877373.119395687990.01508812783480.1807804043190.03982188253620.02134694587120.0329591268585-0.0143363466701-0.09423912962730.0571285727581-0.01209476644640.1009486593240.000370287706780.01686784629620.145258151146-0.01868756782140.14827583882556.69160025525.1533983041116.6393324321
91.67134164370.4373548100440.1028579258175.787296235122.761072979033.73558251545-0.035101625645-0.0652589732196-0.0512703632405-0.06796006509040.139719555563-0.0158013823024-0.08894225071230.0937568607312-0.1025122519230.137543335870.026283219575-0.004635760240330.1219832898330.01400276795180.15833306972749.76225165672.2554724100121.9982445466
102.42673054250.9520396117050.2009994757261.59738029282-0.8418383656851.172202728840.0706894054862-0.0452681653322-0.3926796151350.1355852428380.0549047487774-0.2140312761030.156716955584-0.0237955299189-0.1167436784160.1864412084170.0416028026832-0.002836259485960.11976332261-0.00224755257080.2132661441247.5945283887-7.336541898223.3281724798
115.18884524371-0.0892336518559-1.742518701132.76989552475-0.7289225835623.47570319872-0.100368666345-0.221019051401-0.540490366540.364952838789-0.0140506440872-0.4764885044010.3304385086540.2402886097720.09899248189070.2713467407030.0457189682608-0.07469881199640.1547784403880.04362082351830.29465197935954.0701756546-9.6996023895930.785657567
122.641503447180.377101384668-0.371967606982.78063733042-2.004865020614.34839132438-0.05681843487480.3805214305260.06891323036630.001526198971140.2792996799640.0421006068901-0.151651582498-0.364609753781-0.2395537751040.1187285487830.0430895277658-0.005184655736910.186109349464-0.001210948708580.16324401610942.13091893185.8376780880214.2835429749
133.11594016115-0.38737312025-0.7047543475152.228171425610.6588731846082.432325919710.0144578818910.85214144161-0.0430402577918-0.3669274499240.088576504417-0.0975407248927-0.1328290167390.031310047966-0.03881582245210.180782100847-0.02014703700310.02821313915290.338624211401-0.04021492370110.18046176869555.78423320794.565713723513.84285090519
146.647569531412.78384420637-2.296155858232.02730806501-1.794796115498.586211536250.005457687958730.324810239031-0.3545805629760.365299657399-0.140335416619-0.0294521339405-0.1309315523730.4769736857680.09798452905170.1819801193530.0173124386138-0.0009220832406630.239845519448-0.05161648229960.23427643890964.50260878240.41268805389912.4353316703
155.13591930892-1.425633448352.096668613452.87198363569-2.092415904362.76451306574-0.07877744013770.816207941441-0.0211188788129-0.1475764538640.0883033814925-0.0163975320053-0.1964071331420.1206277407910.006651050197350.190536824788-0.005916718082520.04969871676460.321997338587-0.02502184415620.16302525360953.91823664776.581359103242.04970947792
163.117827092610.438799441986-1.588218331752.19384157828-0.947561367257.05437326123-0.05604383425850.302706157171-0.0820526675612-0.04259094567150.04265440621760.033883586994-0.119827533139-0.07318057397830.02552850861840.126761373325-0.003857314690090.001692838067950.178000112371-0.01607880444850.16669896348145.13861589142.332757150510.9514480451
172.416196549450.5782782462090.1968333052382.49474691122-0.5751508581692.45701919172-0.2167369939340.202945961469-0.234340664459-0.2788207736220.188423864126-0.06648466174440.267537194205-0.4453442833250.02760457761390.362851313584-0.1239806742340.07450156026890.304986534109-0.006685234798940.15821277667824.53316135826.50987639731-11.4094945753
182.12772124981-0.1261410050940.1281589919255.693344799153.168216034894.64335135776-0.164021496650.282467254049-0.163125159942-0.254529048360.0041715450541-0.03387033923380.425595900384-0.25294247750.1558826572950.258217518223-0.07379545551270.04959574401490.1843062111380.006284944912370.13038550947430.35135733189.59083742693-17.8236078722
193.267587964261.21639951778-0.01512470977512.95605608564-0.3041851545842.73461985709-0.1348955276060.130037171927-0.00955387110731-0.05479039499780.0650828702575-0.1283561414040.1065478526740.01441019320440.06797534493450.195946194837-0.0336929778840.02782812821290.1504205528340.002234487074830.11956878138436.518354885717.170933373-15.9802789172
204.980916705150.875685614293-1.038711666774.83278144229-1.180875352465.98564726028-0.135955817832-0.312681863508-0.360670013167-0.161107778543-0.0258661190365-0.4178847229460.2602910904110.4594370670440.1085823932130.1765170902380.0288697737880.02630640886770.2217000695050.04294424155820.23096731574844.369354739911.7083422571-12.1536417866
212.625889776170.233311681881-0.2371874758632.51950481315-0.41250834862.93876046996-0.182129357440.4677729678250.24934955344-0.3910272486470.3372244874560.3418054069650.0917892351746-0.878514350787-0.1532489886340.359556376406-0.0992322054867-0.02087538900950.4717152938130.09703634267560.19071010823621.828562083314.5509890013-23.6018297994
221.62229742410.164598221324-0.3930752387711.9190325004-0.8028756126724.541554612130.06187933019750.1053314148080.278569337650.282961657460.1826494606620.207535124093-0.0375080298694-0.705408902833-0.2417922973880.250612635188-0.0252826014780.05413296018080.3216080067750.06393149309220.26028229626919.25535560516.4648329748-7.68240746239
233.490461842490.3618618204221.481599811133.293150103392.32298168633.662911500560.06964207587570.3034913488830.3076329768520.24695929768-0.09132873248320.5757198315780.146624663092-0.797071527549-0.01150654757020.289505050737-0.05129790743570.08071329520430.4996199625370.04742406918630.32298506083111.678678966812.6212910292-1.21358072964
245.158056019351.016704706560.4199700265554.860766098490.8614747380542.14174658738-0.00777479074860.214778077750.2056829926210.1285548355220.07088753614470.767633656582-0.045968462175-1.07833629332-0.0217913820760.288269951882-0.0460608763170.0481074347340.5683668202160.1115913375480.2664959395512.986075559813.0927422204-11.3425425252
258.051501938812.89934191785-3.265343236488.05539254223-1.948491123697.77463166438-0.09310737685710.0525890014919-0.4916605493570.2108644358370.1827043780090.2769772868410.398779839966-0.359744202637-0.0621981057280.247601898478-0.03480144574370.02738230551330.2486892925560.02710600970150.17973551896123.29011916367.85775598847-1.76978906678
263.48369269749-0.3018846114550.925564874931.481877422710.3878477527631.906673383740.2859319296560.8045688046690.441188046399-0.141533045305-0.2316098596870.481134473996-0.0192001599168-0.959287756603-0.02277225682580.2685219674020.002874104793620.07416652544480.716594916640.09289521390940.35281645177110.480962165614.4703104359-10.4835230182
275.92058205110.0251978226425-2.670897310551.39241164812-0.2593091789343.984701843960.01146056077460.5674221667370.31456660141-0.1492473817340.2504272232460.09947924462470.0305265342708-0.90892155809-0.2342003367770.26880682687-0.022232075287-0.03157851956460.3894929262160.1231924976630.20059950212121.60533545216.8101855006-19.2924300184
283.4281857066-0.383888108420.59175913243.73211313926-1.041504978653.135182340980.10811720657-0.0185522801948-0.0441558937519-0.0120800367257-0.01146173948090.2776698461880.0302115438696-0.0580579827732-0.1064342620520.1192503018590.01610584424620.002370713750940.102858201139-0.04220886810480.0968694084413.006473689912.834564511222.9478177697
291.960870878280.03407300842610.1002053695573.084818466330.05249535541041.69056797142-0.02982314160630.00751306033940.3180996160.00048743455386-0.08731338191340.246613020754-0.154453980663-0.1218905827940.09397228469810.1859801802670.03424877087470.01137003413880.115387272712-0.0223103540680.21994332384411.518160881528.676785564125.7887362394
304.7950404925-0.9755458906820.2448198412272.861362533580.3498525800692.2950697363-0.0568938787806-0.2206775089270.1633295042460.3846354636710.0250656624669-0.2379565525220.06283592863190.126048243560.02587105331350.218035432831-0.007908392163660.008222840075230.171303266562-0.007734723185410.10877432903820.438140664516.442606503734.7322796276
311.459705539710.000208001380941-0.2105039269572.318014192540.0170959312.54678504914-0.01570668583860.0821219462722-0.0546024165819-0.0280211714868-0.0160520897092-0.1403989988480.0959247333520.1099098469230.01729434614990.135942195170.01166559538250.01397192060240.1224751226080.003782956430620.15114504608222.67120409988.6427708835918.4851747022
322.77501383035-0.998092827790.1522493141342.262313138560.3032095196180.811087767153-0.00572498226879-0.08533939904890.05930858923360.1212129227070.0589873083783-0.123618157760.01313632999530.116872760903-0.03777629943830.193576090422-0.00618976589950.02650100886850.1170150373420.01520010605640.15307744682424.870108063411.165295286925.9359280418
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 24 )AA1 - 241 - 27
22chain 'A' and (resid 25 through 42 )AA25 - 4228 - 46
33chain 'A' and (resid 43 through 60 )AA43 - 6047 - 64
44chain 'A' and (resid 61 through 104 )AA61 - 10465 - 111
55chain 'A' and (resid 105 through 128 )AA105 - 128112 - 135
66chain 'A' and (resid 129 through 186 )AA129 - 186136 - 194
77chain 'A' and (resid 187 through 220 )AA187 - 220195 - 229
88chain 'B' and (resid 1 through 24 )BB1 - 241 - 26
99chain 'B' and (resid 25 through 42 )BB25 - 4227 - 45
1010chain 'B' and (resid 43 through 80 )BB43 - 8046 - 83
1111chain 'B' and (resid 81 through 104 )BB81 - 10484 - 110
1212chain 'B' and (resid 105 through 128 )BB105 - 128111 - 134
1313chain 'B' and (resid 129 through 186 )BB129 - 186135 - 193
1414chain 'B' and (resid 187 through 197 )BB187 - 197194 - 204
1515chain 'B' and (resid 198 through 207 )BB198 - 207205 - 215
1616chain 'B' and (resid 208 through 220 )BB208 - 220216 - 228
1717chain 'C' and (resid 2 through 24 )CC2 - 241 - 25
1818chain 'C' and (resid 25 through 42 )CC25 - 4226 - 44
1919chain 'C' and (resid 43 through 80 )CC43 - 8045 - 82
2020chain 'C' and (resid 81 through 104 )CC81 - 10483 - 107
2121chain 'C' and (resid 105 through 128 )CC105 - 128108 - 131
2222chain 'C' and (resid 129 through 144 )CC129 - 144132 - 147
2323chain 'C' and (resid 145 through 154 )CC145 - 154148 - 158
2424chain 'C' and (resid 155 through 186 )CC155 - 186159 - 188
2525chain 'C' and (resid 187 through 197 )CC187 - 197189 - 199
2626chain 'C' and (resid 198 through 207 )CC198 - 207200 - 211
2727chain 'C' and (resid 208 through 220 )CC208 - 220212 - 225
2828chain 'D' and (resid 1 through 24 )DD1 - 241 - 27
2929chain 'D' and (resid 25 through 104 )DD25 - 10428 - 112
3030chain 'D' and (resid 105 through 128 )DD105 - 128113 - 137
3131chain 'D' and (resid 129 through 197 )DD129 - 197138 - 211
3232chain 'D' and (resid 198 through 220 )DD198 - 220212 - 235

+
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