[English] 日本語
Yorodumi
- PDB-8cbu: HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cbu
TitleHIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor MUT884
ComponentsIntegrase
KeywordsVIRAL PROTEIN / Integrase / HIV / ALLINI / Allosteric Inhibitor / Inhibitor / Retrovirus / INLAI / NCINI / MINI / LEDGIN / Mutabilis / MUT884
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / host multivesicular body / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Integrase, C-terminal domain superfamily, retroviral / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral ...Integrase, C-terminal domain superfamily, retroviral / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / SH3 type barrels. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Roll / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Mainly Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Chem-U60 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsSinger, M.R. / Pye, V.E. / Yu, Z. / Cherepanov, P.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Cancer Research UKFC001061 United Kingdom
Medical Research Council (MRC, United Kingdom)FC001061 United Kingdom
Wellcome TrustFC001061 United Kingdom
The Francis Crick InstituteFC001061 United Kingdom
CitationJournal: Antimicrob.Agents Chemother. / Year: 2023
Title: Biological and Structural Analyses of New Potent Allosteric Inhibitors of HIV-1 Integrase.
Authors: Bonnard, D. / Le Rouzic, E. / Singer, M.R. / Yu, Z. / Le Strat, F. / Batisse, C. / Batisse, J. / Amadori, C. / Chasset, S. / Pye, V.E. / Emiliani, S. / Ledoussal, B. / Ruff, M. / Moreau, F. ...Authors: Bonnard, D. / Le Rouzic, E. / Singer, M.R. / Yu, Z. / Le Strat, F. / Batisse, C. / Batisse, J. / Amadori, C. / Chasset, S. / Pye, V.E. / Emiliani, S. / Ledoussal, B. / Ruff, M. / Moreau, F. / Cherepanov, P. / Benarous, R.
History
DepositionJan 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Structure summary / Category: entity / struct / struct_keywords
Item: _entity.details / _struct.title / _struct_keywords.text
Revision 1.2Jun 21, 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 / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jul 26, 2023Group: Database references / Refinement description / Category: citation / struct_ncs_dom_lim
Item: _citation.journal_volume / _struct_ncs_dom_lim.beg_auth_asym_id ..._citation.journal_volume / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrase
B: Integrase
C: Integrase
D: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,07217
Polymers103,6184
Non-polymers1,45413
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.847, 63.559, 69.596
Angle α, β, γ (deg.)90.000, 100.720, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 222 through 248 or resid 250 through 272))
d_2ens_1(chain "C" and (resid 222 through 248 or resid 250 through 272))
d_1ens_2(chain "B" and (resid 57 through 66 or resid 68...
d_2ens_2(chain "D" and (resid 57 through 66 or resid 68...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ASNASNALAALAAA222 - 2484 - 30
d_12ens_1VALVALGLYGLYAA250 - 27232 - 54
d_21ens_1ASNASNALAALACC222 - 2484 - 30
d_22ens_1VALVALGLYGLYCC250 - 27232 - 54
d_11ens_2SERSERTHRTHRBB57 - 6678 - 87
d_12ens_2LEULEUALAALABB68 - 8689 - 107
d_13ens_2VALVALVALVALBB88 - 113109 - 134
d_14ens_2THRTHRILEILEBB115 - 208136 - 229
d_15ens_2EDOEDOEDOEDOBG502
d_16ens_2EDOEDOEDOEDOBH503
d_17ens_2EDOEDOEDOEDOBI504
d_21ens_2SERSERTHRTHRDD57 - 6678 - 87
d_22ens_2LEULEUALAALADD68 - 8689 - 107
d_23ens_2VALVALVALVALDD88 - 113109 - 134
d_24ens_2THRTHRPHEPHEDD115 - 139136 - 160
d_25ens_2GLYGLYILEILEDD149 - 208170 - 229
d_26ens_2EDOEDOEDOEDODO603
d_27ens_2EDOEDOEDOEDODP604
d_28ens_2EDOEDOEDOEDOCL501

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.353026696774, -0.138768950517, -0.92526500514), (-0.409735235991, -0.911994929134, -0.0195521257372), (-0.841123764824, 0.386016097599, -0.378817085996)18.9111218312, -32.1628992613, 41.3613518903
2given(0.473176629276, -0.151033096687, -0.867924467458), (-0.158409081789, -0.983723409553, 0.0848222630204), (-0.866608585414, 0.0973512054485, -0.489399941239)17.1940005109, -35.241769786, 36.0085972122

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Integrase / IN


Mass: 25904.537 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The construct is of HIV-1 integrase with the following domain swap: The C-Terminal Domain of HIV-1 integrase (from residues 220 to 288) is followed by the Catalytic Core Domain of HIV-1 ...Details: The construct is of HIV-1 integrase with the following domain swap: The C-Terminal Domain of HIV-1 integrase (from residues 220 to 288) is followed by the Catalytic Core Domain of HIV-1 integrase (from residues 50 to 212). In addition, there are the following mutations: F185K and W243E. The residue numbers are correct in the structure. Because the linker is not defined in the electron density map, we do not know for sure which CTD is linked to which CCD in the lattice formation. We have therefore kept each domain as a separate chain. This chain is CTD There are 2 copies of CTD and CCD in the asymmetric unit. We cannot determine how they are connected in the crystal lattice.
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag-pol / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P12497, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds

-
Non-polymers , 6 types, 135 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-U60 / (2S)-2-[3-cyclopropyl-6-methyl-2-(5-methyl-3,4-dihydro-2H-chromen-6-yl)phenyl]-2-cyclopropyloxy-ethanoic acid


Mass: 392.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H28O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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

Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 8000, ethylene glycol, magnesium chloride, calcium chloride, imidazole, MES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.44→51.92 Å / Num. obs: 17040 / % possible obs: 99.98 % / Redundancy: 12.43 % / Biso Wilson estimate: 45.36 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.025 / Net I/σ(I): 17.9
Reflection shellResolution: 2.44→2.48 Å / Redundancy: 11.27 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 852 / CC1/2: 0.992 / Rpim(I) all: 0.077 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→51.92 Å / SU ML: 0.3356 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 29.186
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2536 838 4.93 %
Rwork0.2018 16157 -
obs0.2043 16995 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.45 Å2
Refinement stepCycle: LAST / Resolution: 2.44→51.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 99 122 3235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00183225
X-RAY DIFFRACTIONf_angle_d0.4714346
X-RAY DIFFRACTIONf_chiral_restr0.0414478
X-RAY DIFFRACTIONf_plane_restr0.0028536
X-RAY DIFFRACTIONf_dihedral_angle_d14.06731182
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.39884056712
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS3.05274617713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.590.29141310.26332669X-RAY DIFFRACTION99.61
2.59-2.790.30791520.25952673X-RAY DIFFRACTION99.75
2.79-3.070.25351460.21352656X-RAY DIFFRACTION99.82
3.07-3.520.26741270.19982703X-RAY DIFFRACTION99.89
3.52-4.430.20811320.17772708X-RAY DIFFRACTION99.89
4.43-51.920.25821500.19382748X-RAY DIFFRACTION99.79
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)
10.2100988641170.309062053318-0.2190911248151.227980866750.217969848750.2369252842670.0805088526790.323435423895-0.960078958354-0.418257559819-0.07537393910940.040967081363-0.5662893162060.3786022513743.18357185699E-50.549707149194-0.0624763463908-0.04819236108231.00246747137-0.06878645392650.50867301132313.652-14.687-14.407
25.966030575652.785464220061.614712886281.345156110630.7863678415640.476415393165-1.20803872570.058984505595-0.0929515297032-0.718658305874-0.891751045398-0.2506830848120.961573493661-0.536411363254-1.380508593380.997854114316-0.1586516037530.05413396722780.9390009594330.1016187206690.413824594525.027-21.729-20.612
30.4902949619010.0691078068-0.0701725902436-0.05286292732330.008964199598610.511863885833-0.188787298596-0.4951737964140.11324339734-0.3237980129040.169774373067-0.1933637983530.630430954525-0.00334653804717-0.00021197250060.596296306231-0.0263150409026-0.03212452272610.7046353528870.03331571117270.47002673150510.647-17.253-19.104
40.2712887773230.0626875553469-0.6701644809840.0166291922744-0.1564516145661.64905492656-0.680647965360.263094173817-0.594742843403-0.324149848869-0.4834258673571.303338368031.15544120616-0.204395939342-0.03837546278040.5377767153660.026734054224-0.07390509654470.906577899672-0.06498979821140.8204242077951.241-19.197-1.488
50.1950846694790.387489103806-0.2331768387491.18036216651-0.1241869814580.8138187606070.1188703437970.1556257584740.338770164828-0.252277853396-0.168431912545-0.0899546524186-0.4954151343990.05120232269620.0001937748556060.365822175981-0.01612165439020.01777256990160.3123504627880.03430924340050.48059057644719.78-6.26410.015
60.300484669623-0.380725813046-0.08242805515370.3552768302070.3047319380920.270067284339-0.245379474433-0.167114719176-0.183049974552-0.05570325811750.04637136838870.03047349529-0.02368111431920.0328295061098-2.10000760773E-50.4113101226550.0411160171948-0.002815586352490.3846616029980.003703614552050.39388922061820.006-10.56910.612
70.0706067421785-0.151884506213-0.03052389177130.526236840299-0.05899736668460.128043064912-0.455885593634-0.221705195002-0.5791334068620.0323577216607-0.0754973774054-0.8418692524510.9531542240770.655364653003-0.0003664931072850.434145113573-0.002550858102340.0524925528260.3116596155310.03827240675910.44122827960417.885-15.6713.361
80.1532386953830.116619346660.2663632934280.1196089780510.1839088672650.3519445503040.349142068743-0.2097440498870.04559359867540.414051235561-0.3430098809270.629007051502-0.0591127486197-0.1370766657988.60013218437E-50.5560825921440.0767677986038-0.1097863523120.6111076010270.009716562622090.5459885811338.489-10.7358.194
90.02279528262370.052818613962-0.01537345805270.0685884780415-0.01856247972380.0665072941448-0.121678308080.658355131298-0.209307874201-0.921048801808-0.128462023499-0.7318606422730.09446033708270.799097382565-0.0001424733066180.5712736517880.0740382907546-0.06430921446770.4643558398120.06076520045470.4546233134718.2-3.63-1.27
10-0.04421261328250.130377236279-0.09786134625090.465415071344-0.3670079761990.2784695194430.2629067085580.2043663334880.342664492859-0.349214371243-0.3222897876420.709156223464-0.291543345337-0.384481751361-9.41454832767E-50.4748290168890.0788817299043-0.06416267222040.4498011309620.004501231197770.44719211403210.049-10.505-1.968
110.712003918750.613328556785-0.2753938205990.8017843891310.2006537276690.587864550993-0.1494269406130.1371392025210.6282917723870.420436689755-0.100216678951-0.391432874143-0.5595977780010.687124784254-0.0004508586225940.448832321307-0.0434973570294-0.01014401656490.414489298786-0.07590659861280.51293731612325.461-3.68319.421
120.1821697737260.1674290181880.05144673232220.192467808702-0.1893446892270.302914813864-0.409331532128-0.340670742326-0.1427503590070.3819686831790.102347069242-0.0849458881461-0.007977836206250.5402103103577.0451622786E-50.454170189824-0.02314525875870.004819866001130.492073133275-0.02320771941150.42438278981625.944-12.82720.323
130.143331457401-0.2811845282620.2155247503870.493431236201-0.3906699619050.348563252318-0.613064778727-0.1750058132140.1102820466870.977733433077-0.003106717390510.930728643389-0.0224804883655-0.555239427343-0.0613051405670.4785428696620.02239993067810.08832555108910.728294125255-0.2083972702950.53782449176111.004-7.86730.149
140.102837406520.0128250180093-0.114468877865-0.01812101279540.001287088595530.09911960471960.211315298638-0.395374328945-0.5278187972910.3970579153830.2334982597210.255460294372-0.179027012626-0.305517000084-0.000177520738050.4947692984650.06283773149740.007502876967920.596786921910.0512976187360.5135648911143.647-12.30220.471
150.09955481209250.216713380557-0.002045392641790.320826071078-0.045691402188-0.005785779171260.0613905864005-0.114495648371-0.5507039526110.537044873429-0.2373165236030.207391340211-0.427728748056-0.118486315694-0.000927517946630.7692623158220.077208856477-0.118202175321.17498114636-0.1094442590630.55987385056734.413-20.57834.264
160.4649439358980.1558652013270.01378198100790.3115436216050.06003195211820.01270991609930.828963618894-0.433462969295-0.422121752383-0.689898864967-0.0172835407635-0.9142565589411.18633672769-0.4738536751110.02291232415660.728834024661-0.08153886011990.1287810440080.650282849041-0.1211475346970.53048210804541.93-26.81726.89
172.03641539068-0.854632233992-0.1238191499390.4141997131960.118500555450.0991738827625-0.327872402687-0.2620865595560.2752208621060.290489107697-0.122217789492-0.1171893063350.232414995071-1.15859356902-0.09947766126190.599236601734-0.04760853867790.0245544694190.8302377005970.005066907438890.38083421017843.041-18.31736.649
180.0448629823304-0.007104287520630.02370012479430.2922087999980.4075917200950.439619334905-0.2635874415650.0407113073680.2858699669720.210001597529-0.285435991625-0.02730887636060.110974964286-0.259072828344-0.001184368417530.4266377586550.05272190544340.02907701799260.9359235540810.04563268583530.36516268732244.827-19.63230.677
192.365441076083.93065743845-1.196251004666.59157835385-1.984567788990.60791277974-0.3853192192410.7114420491360.855451779910.4044440356570.4994348420591.01482086735-1.097880931350.5221753141830.1495308725370.5358527932950.407566323326-0.2131678995541.52810780156-0.255981976140.42016832716727.006-14.9431.823
201.47544725525-0.197965188346-0.03363921178810.329333312373-0.3666038749291.36221972696-0.0130976776048-0.215249635895-0.3602019172080.01382094378170.0201690716142-0.0488436623830.2271664354850.05314334684152.18657101847E-50.392566840630.00414511511069-0.01585508618250.3798219809320.08571936807290.4411289325320.626-28.3216.229
211.29834290416-0.352701275495-1.678140735861.595891535591.335525857772.582216686180.0950697374813-1.01916435057-0.415656231451-0.05373765146870.607933494989-0.2732283078310.05875002624620.7679239927570.2170453819820.403717618230.0705284418577-0.009527075842660.4633156285070.1890837200260.5732547021524.338-27.74626.783
221.086202671-0.8447839595170.06631696053030.7874917788350.4056274441030.4990290096220.1147215148530.140277158136-0.19806464169-0.2386126265230.006226096599430.3864281562570.12088076892-0.360793562775-1.39523165181E-50.400013669858-0.03479222249170.002864203660910.368485141378-0.05493131232660.45120774437313.329-29.8933.244
230.459722457672-0.4562222895650.04904662235810.44854379086-0.104199266650.1005982494650.0314995450291-0.556424568177-0.008803701807360.0995180790955-0.2873828985270.630022644962-0.408339301091-1.05024219668-0.0002106467460560.399931112128-0.029251802590.05682575991230.7697223600250.0612919682610.5410879576891.397-22.92519.115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 222:239 )A222 - 239
2X-RAY DIFFRACTION2( CHAIN A AND RESID 240:247 )A240 - 247
3X-RAY DIFFRACTION3( CHAIN A AND RESID 248:269 )A248 - 269
4X-RAY DIFFRACTION4( CHAIN A AND RESID 270:274 )A270 - 274
5X-RAY DIFFRACTION5( CHAIN B AND RESID 57:78 )B57 - 78
6X-RAY DIFFRACTION6( CHAIN B AND RESID 79:93 )B79 - 93
7X-RAY DIFFRACTION7( CHAIN B AND RESID 94:105 )B94 - 105
8X-RAY DIFFRACTION8( CHAIN B AND RESID 106:114 )B106 - 114
9X-RAY DIFFRACTION9( CHAIN B AND RESID 115:123 )B115 - 123
10X-RAY DIFFRACTION10( CHAIN B AND RESID 124:149 )B124 - 149
11X-RAY DIFFRACTION11( CHAIN B AND RESID 150:168 )B150 - 168
12X-RAY DIFFRACTION12( CHAIN B AND RESID 169:185 )B169 - 185
13X-RAY DIFFRACTION13( CHAIN B AND RESID 186:195 )B186 - 195
14X-RAY DIFFRACTION14( CHAIN B AND RESID 196:208 )B196 - 208
15X-RAY DIFFRACTION15( CHAIN C AND RESID 221:227 )C221 - 227
16X-RAY DIFFRACTION16( CHAIN C AND RESID 228:239 )C228 - 239
17X-RAY DIFFRACTION17( CHAIN C AND RESID 240:255 )C240 - 255
18X-RAY DIFFRACTION18( CHAIN C AND RESID 256:267 )C256 - 267
19X-RAY DIFFRACTION19( CHAIN C AND RESID 268:272 )C268 - 272
20X-RAY DIFFRACTION20( CHAIN D AND RESID 57:123 )D57 - 123
21X-RAY DIFFRACTION21( CHAIN D AND RESID 124:149 )D124 - 149
22X-RAY DIFFRACTION22( CHAIN D AND RESID 150:185 )D150 - 185
23X-RAY DIFFRACTION23( CHAIN D AND RESID 186:210 )D186 - 210

+
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