[English] 日本語
Yorodumi
- PDB-8dla: ClpP2 from Chlamydia trachomatis bound by MAS1-12 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dla
TitleClpP2 from Chlamydia trachomatis bound by MAS1-12
ComponentsATP-dependent Clp protease proteolytic subunit 2
KeywordsHYDROLASE/INHIBITOR / Protease / Chlamydia trachomatis / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


endopeptidase Clp / ATP-dependent peptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
Chem-UER / ATP-dependent Clp protease proteolytic subunit 2
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsAzadmanesh, J. / Struble, L.R. / Seleem, M.A. / Ouellette, S. / Conda-Sheridan, M. / Borgstahl, G.E.O.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1P20GM121316-01A1 United States
Department of Defense (DOD, United States)PRMRP#PR172445 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)5P30CA036727-33 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: The structure of caseinolytic protease subunit ClpP2 reveals a functional model of the caseinolytic protease system from Chlamydia trachomatis.
Authors: Azadmanesh, J. / Seleem, M.A. / Struble, L. / Wood, N.A. / Fisher, D.J. / Lovelace, J.J. / Artigues, A. / Fenton, A.W. / Borgstahl, G.E.O. / Ouellette, S.P. / Conda-Sheridan, M.
History
DepositionJul 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit 2
B: ATP-dependent Clp protease proteolytic subunit 2
C: ATP-dependent Clp protease proteolytic subunit 2
D: ATP-dependent Clp protease proteolytic subunit 2
E: ATP-dependent Clp protease proteolytic subunit 2
F: ATP-dependent Clp protease proteolytic subunit 2
G: ATP-dependent Clp protease proteolytic subunit 2
H: ATP-dependent Clp protease proteolytic subunit 2
I: ATP-dependent Clp protease proteolytic subunit 2
J: ATP-dependent Clp protease proteolytic subunit 2
K: ATP-dependent Clp protease proteolytic subunit 2
L: ATP-dependent Clp protease proteolytic subunit 2
M: ATP-dependent Clp protease proteolytic subunit 2
N: ATP-dependent Clp protease proteolytic subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,49232
Polymers309,00114
Non-polymers3,49218
Water8,467470
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.000, 98.010, 97.970
Angle α, β, γ (deg.)97.160, 114.150, 114.160
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 10 or resid 12...
d_2ens_1(chain "B" and (resid 2 through 10 or resid 12...
d_3ens_1(chain "C" and (resid 2 through 10 or resid 12...
d_4ens_1(chain "D" and (resid 2 through 10 or resid 12...
d_5ens_1(chain "E" and (resid 2 through 10 or resid 12...
d_6ens_1(chain "F" and (resid 2 through 10 or resid 12...
d_7ens_1(chain "G" and (resid 2 through 10 or resid 12...
d_8ens_1(chain "H" and (resid 2 through 10 or resid 12...
d_9ens_1(chain "I" and (resid 2 through 10 or resid 12...
d_10ens_1(chain "J" and (resid 2 through 10 or resid 12...
d_11ens_1(chain "K" and (resid 2 through 10 or resid 12...
d_12ens_1(chain "L" and (resid 2 through 10 or resid 12...
d_13ens_1(chain "M" and (resid 2 through 10 or resid 12...
d_14ens_1(chain "N" and (resid 2 through 10 or resid 12...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRASPA2 - 10
d_12ens_1GLYGLYA12
d_13ens_1GLYGLYA14
d_14ens_1ARGGLYA16 - 127
d_15ens_1ILEILEA129
d_16ens_1ALAALAA134
d_17ens_1ILEILEA136
d_18ens_1LEUALAA138 - 193
d_19ens_1THRTHRA196
d_21ens_1THRASPC2 - 10
d_22ens_1GLYGLYC12
d_23ens_1GLYGLYC14
d_24ens_1ARGGLYC16 - 127
d_25ens_1ILEILEC129
d_26ens_1ALAALAC134
d_27ens_1ILEILEC136
d_28ens_1LEUALAC138 - 193
d_29ens_1THRTHRC196
d_31ens_1THRASPE2 - 10
d_32ens_1GLYGLYE12
d_33ens_1GLYGLYE14
d_34ens_1ARGGLYE16 - 127
d_35ens_1ILEILEE129
d_36ens_1ALAALAE134
d_37ens_1ILEILEE136
d_38ens_1LEUALAE138 - 193
d_39ens_1THRTHRE196
d_41ens_1THRASPH2 - 10
d_42ens_1GLYGLYH12
d_43ens_1GLYGLYH14
d_44ens_1ARGGLYH16 - 127
d_45ens_1ILEILEH129
d_46ens_1ALAALAH134
d_47ens_1ILEILEH136
d_48ens_1LEUALAH138 - 193
d_49ens_1THRTHRH196
d_51ens_1THRASPJ2 - 10
d_52ens_1GLYGLYJ12
d_53ens_1GLYGLYJ14
d_54ens_1ARGGLYJ16 - 127
d_55ens_1ILEILEJ129
d_56ens_1ALAALAJ134
d_57ens_1ILEILEJ136
d_58ens_1LEUALAJ138 - 193
d_59ens_1THRTHRJ196
d_61ens_1THRASPK2 - 10
d_62ens_1GLYGLYK12
d_63ens_1GLYGLYK14
d_64ens_1ARGGLYK16 - 127
d_65ens_1ILEILEK129
d_66ens_1ALAALAK134
d_67ens_1ILEILEK136
d_68ens_1LEUALAK138 - 193
d_69ens_1THRTHRK196
d_71ens_1THRASPL2 - 10
d_72ens_1GLYGLYL12
d_73ens_1GLYGLYL14
d_74ens_1ARGGLYL16 - 127
d_75ens_1ILEILEL129
d_76ens_1ALAALAL134
d_77ens_1ILEILEL136
d_78ens_1LEUALAL138 - 193
d_79ens_1THRTHRL196
d_81ens_1THRASPO2 - 10
d_82ens_1GLYGLYO12
d_83ens_1GLYGLYO14
d_84ens_1ARGGLYO16 - 127
d_85ens_1ILEILEO129
d_86ens_1ALAALAO134
d_87ens_1ILEILEO136
d_88ens_1LEUALAO138 - 193
d_89ens_1THRTHRO196
d_91ens_1THRASPP2 - 10
d_92ens_1GLYGLYP12
d_93ens_1GLYGLYP14
d_94ens_1ARGGLYP16 - 127
d_95ens_1ILEILEP129
d_96ens_1ALAALAP134
d_97ens_1ILEILEP136
d_98ens_1LEUALAP138 - 193
d_99ens_1THRTHRP196
d_101ens_1THRASPQ2 - 10
d_102ens_1GLYGLYQ12
d_103ens_1GLYGLYQ14
d_104ens_1ARGGLYQ16 - 127
d_105ens_1ILEILEQ129
d_106ens_1ALAALAQ134
d_107ens_1ILEILEQ136
d_108ens_1LEUALAQ138 - 193
d_109ens_1THRTHRQ196
d_111ens_1THRASPR2 - 10
d_112ens_1GLYGLYR12
d_113ens_1GLYGLYR14
d_114ens_1ARGGLYR16 - 127
d_115ens_1ILEILER129
d_116ens_1ALAALAR134
d_117ens_1ILEILER136
d_118ens_1LEUALAR138 - 193
d_119ens_1THRTHRR196
d_121ens_1THRASPS2 - 10
d_122ens_1GLYGLYS12
d_123ens_1GLYGLYS14
d_124ens_1ARGGLYS16 - 127
d_125ens_1ILEILES129
d_126ens_1ALAALAS134
d_127ens_1ILEILES136
d_128ens_1LEUALAS138 - 193
d_129ens_1THRTHRS196
d_131ens_1THRASPT2 - 10
d_132ens_1GLYGLYT12
d_133ens_1GLYGLYT14
d_134ens_1ARGGLYT16 - 127
d_135ens_1ILEILET129
d_136ens_1ALAALAT134
d_137ens_1ILEILET136
d_138ens_1LEUALAT138 - 193
d_139ens_1THRTHRT196
d_141ens_1THRASPV2 - 10
d_142ens_1GLYGLYV12
d_143ens_1GLYGLYV14
d_144ens_1ARGGLYV16 - 127
d_145ens_1ILEILEV129
d_146ens_1ALAALAV134
d_147ens_1ILEILEV136
d_148ens_1LEUALAV138 - 193
d_149ens_1THRTHRV196

NCS oper:
IDCodeMatrixVector
1given(0.912122471355, 0.295620647525, 0.283973643156), (0.144898223036, -0.880552711148, 0.451255390939), (0.383454172243, -0.370452906113, -0.846006821569)6.71138258006, -56.2287980013, -0.871216032611
2given(0.982589662505, 0.184975530524, -0.0173668721045), (-0.101725320202, 0.613862685844, 0.78283111982), (0.155465476454, -0.767435115196, 0.62199182438)5.40787073853, -15.1999993784, -20.2845225529
3given(-0.938917772196, 0.0144401486851, -0.343838478302), (0.0399095745241, -0.987809332316, -0.150465773023), (-0.34181960581, -0.154997435772, 0.926895437462)95.8752382778, -44.6796508802, 13.4045308161
4given(-0.94361062334, -0.318375750179, -0.0907517119302), (-0.316864544335, 0.789155790006, 0.526146367129), (-0.0958950054158, 0.525233301303, -0.845537773928)85.5260323239, 2.94599096874, 42.1362791508
5given(0.983437788837, -0.0960035272023, 0.153731708673), (0.179447465789, 0.634938838135, -0.751432817256), (-0.025470031577, 0.766574193795, 0.641650436686)-3.65479527409, -6.23563664517, 23.3924561674
6given(-0.914624358456, -0.145683826776, -0.377145204842), (-0.149250069987, -0.745276850368, 0.649836004631), (-0.375748186328, 0.650644787054, 0.659905039798)92.0809631867, -41.6128930735, 37.1798265588
7given(-0.999970332722, -0.00478597383529, 0.00603557200549), (-0.00735504872658, 0.360470074516, -0.932741780257), (0.00228843466482, -0.932758500274, -0.360494581421)93.7716849082, -1.09055792985, -2.51827096608
8given(-0.912146261805, -0.298512731955, -0.28085467049), (-0.304871217404, 0.036165549155, 0.951706674272), (-0.273939295965, 0.953720190578, -0.123996210469)87.3449883699, -21.1064375808, 50.2185449221
9given(-0.982715705127, -0.182765518807, 0.0294382069966), (-0.18298556844, 0.934933376569, -0.303999774867), (0.0280379143032, -0.304132120158, -0.952217164753)88.7525931954, 11.8200135759, 19.1164895814
10given(0.943561087625, -0.0333046448231, 0.329519763524), (0.315602784419, -0.211297856551, -0.92506653722), (0.100435832184, 0.976854142874, -0.1888613967)-2.85897173185, -30.0026326364, 33.6723165335
11given(0.944646084588, 0.314928589357, 0.0919986873674), (-0.0245700106038, -0.211714169798, 0.977022735092), (0.327169817451, -0.925201109982, -0.192257162771)8.35043314596, -39.9483277927, -20.2391331219
12given(-0.980583190411, 0.100953993773, -0.168121675654), (0.0959992130168, -0.50044357161, -0.860430347404), (-0.170999291763, -0.859863083738, 0.481035050117)97.9405155105, -26.7308958122, -4.55123716487
13given(0.90759030027, 0.144427470945, 0.394234134104), (0.306577179742, -0.869512620621, -0.387244413055), (0.286862823868, 0.472322462114, -0.833439387157)2.06578057205, -51.4449324897, 22.7275643108

-
Components

#1: Protein
ATP-dependent Clp protease proteolytic subunit 2 / Endopeptidase Clp 2


Mass: 22071.467 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Gene: clpP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3KKY8, endopeptidase Clp
#2: Chemical
ChemComp-UER / 1-{4-[(4-chlorophenyl)methyl]piperazin-1-yl}-2-methyl-2-[5-(trifluoromethyl)pyridine-2-sulfonyl]propan-1-one


Mass: 489.939 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H23ClF3N3O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 46.6% v/v pH 7.0 TacsimateTM (Hampton Research) and 0.5 mM polyoxotungstate [TeW6O24]6- (TEW) (Jena Biosciences)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.66→33.09 Å / Num. obs: 63377 / % possible obs: 90.8 % / Redundancy: 1.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.112 / Net I/σ(I): 5.1
Reflection shellResolution: 2.66→2.86 Å / Num. unique obs: 3388 / CC1/2: 0.556

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JCT

4jct


Resolution: 2.66→33.09 Å / Cross valid method: FREE R-VALUE / σ(F): 57.82 / Phase error: 20.9041
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.21 2184 3.45 %
Rwork0.1735 61193 -
obs0.1749 63377 78.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.08 Å2
Refinement stepCycle: LAST / Resolution: 2.66→33.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21588 0 224 470 22282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005522092
X-RAY DIFFRACTIONf_angle_d1.161429844
X-RAY DIFFRACTIONf_chiral_restr0.05343500
X-RAY DIFFRACTIONf_plane_restr0.01443784
X-RAY DIFFRACTIONf_dihedral_angle_d10.91513096
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.70713333517
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.47182428169
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.49359023231
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS1.59477177613
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS1.57181545219
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS1.84737793178
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS1.65809820204
ens_1d_9AX-RAY DIFFRACTIONTorsion NCS1.7161509009
ens_1d_10AX-RAY DIFFRACTIONTorsion NCS1.65721240318
ens_1d_11AX-RAY DIFFRACTIONTorsion NCS1.44233474506
ens_1d_12AX-RAY DIFFRACTIONTorsion NCS1.44021494084
ens_1d_13AX-RAY DIFFRACTIONTorsion NCS1.47756951091
ens_1d_14AX-RAY DIFFRACTIONTorsion NCS1.45630861371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.720.2792140.2792448X-RAY DIFFRACTION8.19
2.72-2.790.3685250.2517934X-RAY DIFFRACTION17.43
2.79-2.860.297510.23381916X-RAY DIFFRACTION35.63
2.86-2.950.28071240.20623289X-RAY DIFFRACTION60.59
2.95-3.040.22411510.19714509X-RAY DIFFRACTION83.83
3.04-3.150.25691660.19784950X-RAY DIFFRACTION91.8
3.15-3.280.24861800.1924942X-RAY DIFFRACTION91.88
3.28-3.430.24051460.17585041X-RAY DIFFRACTION92.77
3.43-3.610.21361710.17324971X-RAY DIFFRACTION92.59
3.61-3.830.21791540.16135044X-RAY DIFFRACTION93.1
3.83-4.130.20121720.15855015X-RAY DIFFRACTION93.01
4.13-4.540.16731620.14345036X-RAY DIFFRACTION93.52
4.54-5.20.17611710.15345100X-RAY DIFFRACTION93.8
5.2-6.540.18831620.19855078X-RAY DIFFRACTION93.98
6.54-33.090.1951840.17365071X-RAY DIFFRACTION94.06
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)
10.922303721119-0.318155027077-0.2024614589731.19561435518-0.4231880974421.31368443696-0.136946081454-0.00583040665972-0.220717905632-0.1484135233640.2077325921940.2757967706420.00111482560776-0.2404831867960.04609948337960.166544785699-0.1137416469850.007053811786640.3086168846970.03249248293930.29302603547131.4374459707-54.68027420264.74564946228
20.6580222695260.2506971687640.05093645264471.607192515110.06825943335760.999860311712-0.06169527779040.123513380941-0.168586443945-0.3314192313730.1877452581690.216631616875-0.0944482090075-0.2746773150850.02510475488880.132420102324-0.00794088242508-0.03476624104640.2794352025040.09119418253390.24398673300920.566794753-1.7881729184527.5146250948
30.98396891208-0.3558229094780.3285759755461.175526967720.08099674479851.96393868645-0.1267442979710.0113169742918-0.0924317578306-0.06130045770080.08154896549330.1974487618750.00321122224106-0.4203935772480.06384584754230.173781203531-0.06366886640930.04858518720010.2369267546170.007912070416020.26575079539826.0279134887-48.121152688129.0222921775
41.40252037512-0.570216957983-0.3335587050191.06541807746-0.3164349311641.38774329052-0.150782136513-0.3805597173810.1059989837290.002097307607290.169865032044-0.348784507609-0.009224489730980.08451998006410.000107148709730.15735473923-0.0626600676107-0.004259594300310.2050942226740.005357378464720.26201361714563.96703776749.5909973109215.4023439728
50.803825413347-0.1663032262560.20259369350.6307441020830.09462467738130.774441928094-0.124318775039-0.08212247941510.162423689740.0542064374019-0.107982599354-0.3083295075770.08545213629120.0729267452229-0.2345590283460.002662261456870.0142438753387-0.06592896859430.2622192959930.10106339490.37668128151772.6201637465-47.50778174266.78453192722
60.650723887016-0.118041920257-0.1052396983280.3350034111520.02795820948990.515509851815-0.130092631496-0.08544957517180.152202307874-0.0713648109205-0.01201698541210.2634913013470.0600322852172-0.214703416734-0.2575416700350.0370087950743-0.150417005203-0.2296195639920.39695702665-0.1707191057640.23888464165433.0011885742-38.2197899048-16.0023793244
71.43335326748-0.6103384445870.3012738935231.475946632470.2826187682471.52840884847-0.0515851868627-0.0821142312369-0.106640398687-0.01395572640310.160149404523-0.246392031119-0.07668015264940.253607799438-0.03331897887870.119904411674-0.0546559555190.02824114923410.21950996464-0.008453693872390.1975227473569.183404477-2.91522197148-7.66727338197
81.571271606380.11775770587-0.817298974591.457812807340.004535449824721.58569542128-0.1240255632410.121561996748-0.1789812004770.1631557920360.0964261196285-0.3400024408270.1845079581490.258180103960.02043101895670.1947161193310.047215082317-0.07906376317840.299908356491-0.003118350513790.16000723261262.6950183812-24.918079596246.7200493972
90.8365671242920.5856553291710.7761590251.97989181818-0.3700194559292.21255696516-0.05054563207970.04303365282810.092038443014-0.00524949135825-0.148846720057-0.08754605930080.1093452043880.1832908099440.04006869724950.120036077482-0.0006112103256240.04320839158340.2911094817650.01639843206770.22136697694273.5001887422-28.5255303121-10.9489287977
101.330973482070.535087076053-0.783893330592.286519028410.04064967774071.47797588102-0.1421345672280.08543144954930.074644383005-0.01488313810370.145863435909-0.2577522577860.1536786923430.179921607181-0.01174727666770.1916121875170.0918110978472-0.01550326463550.2791013752090.0476895392890.2493674534867.9901025427-45.907268417932.0252943086
111.029495752930.0999474023258-0.599386951241.999596921740.1025962919821.460015010260.125186755137-0.0158203196998-0.06026896235830.0905519576549-0.1518493643810.176523582023-0.0540425625663-0.1135557472160.03809393749430.1477971712830.0325325759246-0.05269911533580.203086843939-0.06805678287380.20738910671430.1460066533-12.8510030748-17.0297015999
120.872365435315-0.1038644640830.5321657213911.514437387520.2686477263741.12873802089-0.1473521522790.272416615768-0.06548014697620.0306899050832-0.06541544143450.271205290625-0.161349438249-0.0619219465835-0.03658682085460.267271379509-0.04505174654060.1105142551820.216571521252-0.007472817904320.17663127405221.2946763877-24.638500366539.7769351787
131.4675852168-0.489104046799-1.03534757151.40802227601-0.1884048676561.75334751373-0.0769179052655-0.201158985325-0.2648959155950.000287887448259-0.00844247449508-0.219947315735-0.04462125669460.244249933960.01129834646370.116185457452-0.0147455529921-0.0306981208490.17717356268-0.006456990986470.14813259862960.7732574115-0.44985873049839.0484935514
140.4077308752780.161919321451-0.1714787323031.5192994908-0.2729278849711.661236372650.06188025302410.1520551589-0.286419722066-0.01289043775810.04132166927850.09959497042730.208555460527-0.190906425560.04956223129270.1700290701650.0767758876155-0.02800794358460.2063548330930.02190572598590.23420631104924.44317748083.691414421072.22571907362
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 1 - 203 / Label seq-ID: 1 - 203

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 1 through 203)AA
22(chain 'B' and resid 1 through 203)BC
33(chain 'C' and resid 1 through 203)CE
44(chain 'D' and resid 1 through 203)DH
55(chain 'E' and resid 1 through 203)EJ
66(chain 'F' and resid 1 through 203)FK
77(chain 'G' and resid 1 through 203)GL
88(chain 'H' and resid 1 through 203)HO
99(chain 'I' and resid 1 through 203)IP
1010(chain 'J' and resid 1 through 203)JQ
1111(chain 'K' and resid 1 through 203)KR
1212(chain 'L' and resid 1 through 203)LS
1313(chain 'M' and resid 1 through 203)MT
1414(chain 'N' and resid 1 through 203)NV

+
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