[English] 日本語
Yorodumi
- PDB-7lri: Structure of HIV-1 Reverse Transcriptase in complex with DNA, dTT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lri
TitleStructure of HIV-1 Reverse Transcriptase in complex with DNA, dTTP, and CA(2+) ion
Components
  • (Reverse transcriptase ...) x 2
  • DNA/RNA (38-MER)
KeywordsTRANSFERASE/DNA / Human immunodeficiency virus 1 / Protein/dsDNA / Aptamer / dNTP / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
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 ...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. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / 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. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsHoang, A. / Ruiz, F.X. / Arnold, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI027690 United States
CitationJournal: Drug Discov Today / Year: 2022
Title: Structural basis of HIV inhibition by L-nucleosides: Opportunities for drug development and repurposing.
Authors: Ruiz, F.X. / Hoang, A. / Dilmore, C.R. / DeStefano, J.J. / Arnold, E.
History
DepositionFeb 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jul 6, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Reverse transcriptase p66
B: Reverse transcriptase p51
C: Reverse transcriptase p66
D: Reverse transcriptase p51
E: DNA/RNA (38-MER)
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,27417
Polymers249,5776
Non-polymers1,69711
Water1,74797
1
A: Reverse transcriptase p66
B: Reverse transcriptase p51
E: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,86711
Polymers124,7893
Non-polymers1,0798
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Reverse transcriptase p66
D: Reverse transcriptase p51
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,4076
Polymers124,7893
Non-polymers6183
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.423, 131.073, 129.847
Angle α, β, γ (deg.)90.000, 101.549, 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

-
Components

-
Reverse transcriptase ... , 2 types, 4 molecules ACBD

#1: Protein Reverse transcriptase p66


Mass: 63874.133 Da / Num. of mol.: 2 / Mutation: C280S, D498N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Production host: Escherichia coli (E. coli)
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H
#2: Protein Reverse transcriptase p51


Mass: 50096.539 Da / Num. of mol.: 2 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03366

-
DNA chain , 1 types, 2 molecules EF

#3: DNA chain DNA/RNA (38-MER)


Mass: 10817.920 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 5 types, 108 molecules

#4: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N2O14P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 10-12% PEG 8000, 50 MM BISTRIS-PROPANE PH 7.2, 50 MM AMMONIUM SULFATE, 5% GLYCEROL, 5% SUCROSE

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 55508 / % possible obs: 99.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 77.96 Å2 / CC1/2: 0.912 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.052 / Rrim(I) all: 0.127 / Net I/σ(I): 14.22
Reflection shellResolution: 3.05→3.1 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.01 / Mean I/σ(I) obs: 1.44 / Num. unique obs: 2697 / CC1/2: 0.597 / Rpim(I) all: 0.464 / Rrim(I) all: 0.01 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D3G

5d3g


Resolution: 3.05→47.18 Å / SU ML: 0.4255 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1829
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2436 1999 3.61 %
Rwork0.2107 53428 -
obs0.2119 55427 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 102.47 Å2
Refinement stepCycle: LAST / Resolution: 3.05→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15818 1440 100 97 17455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002817951
X-RAY DIFFRACTIONf_angle_d0.566424689
X-RAY DIFFRACTIONf_chiral_restr0.04342684
X-RAY DIFFRACTIONf_plane_restr0.0042852
X-RAY DIFFRACTIONf_dihedral_angle_d19.35986860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.120.35791380.3213671X-RAY DIFFRACTION95.54
3.12-3.210.33141410.29723773X-RAY DIFFRACTION98.49
3.21-3.30.3251420.28273825X-RAY DIFFRACTION98.76
3.3-3.410.29981410.26863752X-RAY DIFFRACTION98.53
3.41-3.530.32491430.24753811X-RAY DIFFRACTION99.1
3.53-3.670.25491420.23123801X-RAY DIFFRACTION99.05
3.67-3.840.22461430.22223837X-RAY DIFFRACTION99.23
3.84-4.040.21431430.20653810X-RAY DIFFRACTION99.32
4.04-4.30.22221440.18883843X-RAY DIFFRACTION99.35
4.3-4.630.21761420.17623825X-RAY DIFFRACTION99.32
4.63-5.090.21471440.18263834X-RAY DIFFRACTION99.52
5.09-5.830.25021450.19923874X-RAY DIFFRACTION99.65
5.83-7.340.24451440.21743866X-RAY DIFFRACTION99.78
7.34-47.180.21361470.18183906X-RAY DIFFRACTION98.61
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)
13.70107301693-3.050131899570.839317553185.55751370894-2.861959398036.60580447324-0.01199342954010.896353839570.318597752531-1.18378140193-0.100466429539-0.108340781341-0.651655282504-0.1258621863030.08216623305151.64283231408-0.209555692208-0.08704281016210.7785954141160.1276492089610.6203072436941.8753305011226.1810123135143.496185758
22.191569223960.0290514098171-0.4928505917762.480792188560.03401582637222.11678967460.0428012293136-0.1310057935670.577042924885-0.9198831452760.215266035745-0.126471634011-0.5908062716980.266120792536-0.2196160616720.980422815128-0.1987749686340.09118748190850.507792111497-0.0862933154490.7878192084917.9229694531325.0654206542165.810968062
35.836307667441.30710402479-2.178344148741.47780154533-0.8888829386641.6239808579-0.0819331487173-0.6259265999330.0449387552565-0.009632336206670.06579435161360.147192291752-0.1096807164260.09999120860940.01056969047340.3166477924530.0112199265646-0.01317634721960.658907391381-0.08059865802890.467554096056-13.39079458733.79719178819192.906970558
42.72161422832-2.95957003834-2.964634343695.54722556312.39352476283.98208389373-0.0430077454079-0.5383236664-0.397904804992-0.415069451909-0.4712070308010.9859705952440.161370418637-0.574956131680.5337919313320.4273548269550.0231442696718-0.002002713150590.7482663527220.04937618715950.921670101064-29.2988311922-5.82640126339196.685875818
54.91261681417-0.5699451095161.053104175572.76945382761-0.5502241607866.85643544176-0.07525612007990.0241481948054-0.16646412391-0.5679129929730.150172716478-0.362837962367-0.2081654768290.604978496315-0.08652314437090.552270778972-0.1126917770970.1897638611960.378047103745-0.08075559807020.6383778844511.876359154-4.35093879451162.950325519
61.628246057440.734902641591-0.4280858516976.47145762788-0.5478667500861.81051868548-0.2626374522780.171587120013-0.397978859233-1.048438331960.32058825472-0.2804006599190.4007600383920.444506006154-0.08288500611660.779797677443-0.08439626208780.2110725967690.587355903643-0.150315905690.83232809368711.9938020592-15.6788819317160.427091206
73.06908324009-3.05631088154-0.2881613272494.253551901512.011347689282.35399934463-0.384271515988-0.835239045156-0.42328880931-0.4212111348020.201189432456-0.9218935145760.7000405185771.599563932190.2434256725030.5955066947180.23191520280.07390586972321.034844839110.1040809867880.94973701724611.0635426364-28.4648905623176.956119749
83.995640409290.102432022572-3.666569425990.7735057442691.00104052754.13286362167-0.454304470194-0.0883087971523-1.114096049650.15702090179-0.1655569339230.4589168657360.673519258643-0.4762247831870.7687707026330.69008302270.0663694287190.2768209345030.7347973626160.06376702575621.15698306653-22.6203228524-27.5963932994191.126415003
94.346804920141.339013552131.425783810616.52874137943.859729202545.17535967711-0.162592036386-0.470015537595-0.372210308540.00172894893142-0.1402941075590.4501366360650.335709605392-0.04174042399870.2487469856830.3147680450670.05734736990150.05491219697050.4476936376290.07311270801520.647639586906-2.62663084633-14.4084348158181.194857473
102.687950813130.759332205573-1.310974617275.47936823529-0.412805976068.53200340491-0.3212155287751.64734800076-0.0544297791753-0.6410609978670.5359235090271.246768860730.0889893263094-1.84871621265-0.2030445896061.45684742069-0.0124722599277-0.3149511820532.12376165292-0.1154285803420.924493975422-15.9013114846-55.108731461106.274616411
113.02772625505-1.9445691713-0.8555067440423.97668885405-2.115587584552.511423608280.5256547574291.64339846704-0.114847389921-1.10633018603-0.07974348721741.1567962860.0723677139212-1.11053008078-0.4167752286871.219863445240.163733935636-0.05477541364621.701579974530.1486269827740.85343583386-9.27018714204-49.5170937233113.09472866
124.266423504850.114961439611-1.606179860976.24951106301-1.941508080071.356811605620.813523502752.018632939190.919525089492-1.17363422721-0.2894980433750.137795333217-0.974240207749-0.603881281482-0.2212700950371.683906527480.4662092201180.2869156332841.702925253750.5051360721780.866319049203-0.466542589533-37.9951958726115.447527328
135.75980054082.06438551099-1.495382076284.02164220962-1.015169506513.818759244040.6527789019771.057481045831.22356642362-0.334101847102-0.2150987675930.751584523491-0.894585876739-1.3755890122-0.4445771963660.9194832653330.4465249337370.152687294371.302424507850.2185675262081.05204814109-23.594960704-37.4210041933137.335630085
143.94496461723-0.566951430621-2.257814657754.47480546385-2.340941726438.409331500050.08485388461840.07757520066820.4827917920740.06090988481880.0748557240865-0.350798642575-0.671027979251-0.296698837605-0.1050041814890.436707571786-0.0399011498960.08417468018350.337662665742-0.05774027039080.643788748341-9.4472461566-41.7963678135153.61334625
153.33740757533-0.114701523914-0.04749284442062.8024945562-0.4767692648184.22987375408-0.102835925905-0.143915955063-0.0149519002102-0.1225916680990.1329622061130.1681834263740.0948819331585-0.354254734714-0.03267656241310.220165355431-0.05068374618-0.005551970972160.5735826981590.01221441194670.522204447015-24.6401988817-62.9418014278171.607561647
166.486363258450.274781468421-0.3422467203482.48870265542-1.490194826785.650302663170.0704374196004-0.189558755569-0.5767410170450.0416266207526-0.1144432090640.3991488539430.370168047396-0.421795954664-0.02267507914470.312623282979-0.0107154056838-0.006947413585460.6653110715640.01130424944730.621252088311-23.1937386355-65.0495391733173.97932366
177.5959555482-0.346164426844-0.9951798642296.577259663641.281639599327.3669294052-0.0221928420050.405673435304-0.188181350855-0.4402155979670.125277637473-0.7077964313270.5943311765150.534630904327-0.1575461958390.6435514081460.09680747786580.1776138277170.618456523090.03597775589760.5754519610810.2484790669-60.0157348445133.842884809
181.16433503705-0.1881213221130.5659868839451.40135700987-1.548822482324.465556989550.10640853852-0.0741683859629-0.0661533764011-0.375871297491-0.10340576821-0.4114068298480.4557761533761.21407979933-0.0063884968520.7830656319420.2072977832530.2801868664341.138176916940.05711982883490.83901065055222.5202621494-66.0227510198140.793429575
195.47674254290.930417138801-4.816559095290.848769609007-1.506554330847.38321798052-1.13747837492-0.9451199906350.162942849736-0.4990046621250.256126514203-0.3200471931741.918540451631.87612055640.6416869862490.682380329824-0.03385487047360.1437567257540.980690245060.008753140198250.8782203808713.1024946414-65.9154538515167.661471777
203.34328505627-0.0408630043617-1.105171236222.05010535542-2.072064960364.56558934060.0756586179154-0.257833006418-0.422545686103-0.278735964762-0.190920639828-0.0187030293020.3497316962460.1056091048040.2201094449770.381475040834-0.0306356161355-0.02221459243680.499810327583-0.008955478912370.601068302368-0.733725581142-72.8241927569172.772452331
216.38698418231-3.849980581820.7262635556158.14298310836-1.461595902377.87573513125-0.273613964082-0.0847990383603-0.4594255884870.100221822129-0.1426412685810.3324363347530.4503957840640.05782054735510.406856404010.415889486034-0.06098438209150.08408591166660.391494479354-0.02370201663820.5221518489283.82934098472-61.9781921736154.983250034
227.40189894724-3.46504782723-3.768819057362.308751441240.2807845086819.32383842404-0.1373649097180.0631185405110.869832059284-1.189220130090.1960259817840.706225864107-0.557278943027-0.078136452058-0.07182533888090.999479341006-0.20653489422-0.2548668474050.417593898618-0.02532260102250.911273769039-7.001244738218.5202233521165.697734801
234.97356418373-4.35748990887-5.776370248884.461639512545.507948253047.0284431798-1.715028169650.276205999737-2.11186504813-0.898849007514-0.1311324595230.439250551551.44766510731-0.4291979041741.651097044751.38888025127-0.3630477326020.09128660946151.14888628668-0.0106439544921.12602815108-23.8040196072-2.83600843906173.839472273
244.616559601316.25638893896-2.294213030438.72316147944-1.767978640945.00688471208-1.17512146095-0.118898137862-0.34962130318-2.762325944430.44900595747-0.06390024883730.506298797942-0.4780698965520.871102200811.09425580415-0.1259399877740.04822711920090.7068922887620.1077462885561.04446144086-8.420725586215.6801709108169.111976486
254.769279591022.16336359825-1.021487469894.881229128770.1293527143590.229301627908-0.1702865335441.47222090240.456766051495-0.2215277672810.8582629289040.8063096389560.3441819972750.0586821963175-0.6132870546890.7747166665720.103319940135-0.06442637238541.421423464270.008429132917760.792256227051-18.1375870799-58.8980350034135.960763083
263.16649848423-1.33521814517-3.592583196934.313724563476.140667136149.788054822281.26929439640.0761822174139-1.416191423964.78115904878-2.56368587868-5.625331314081.836507456932.183399668750.7744671814861.23779158765-0.105741181587-0.4959133231671.238720685280.2706451259551.98587559423-19.5944640215-73.3232141274157.084037371
272.96078866428-3.578809960750.4916664454847.26321003169-1.11265407672.372791391590.9579398641871.26528107634-0.160057073765-1.24203034806-0.8777040353171.07009246050.4985788142230.5020459184340.1027967229860.973043013886-0.24865892463-0.05862656897941.549974641050.121308787790.930763878529-18.3556407413-54.1718364441135.497369723
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 83 )AA1 - 831 - 83
22chain 'A' and (resid 84 through 325 )AA84 - 32584 - 325
33chain 'A' and (resid 326 through 515 )AA326 - 515326 - 515
44chain 'A' and (resid 516 through 554 )AA516 - 554516 - 554
55chain 'B' and (resid 4 through 83 )BC4 - 831 - 80
66chain 'B' and (resid 84 through 174 )BC84 - 17481 - 171
77chain 'B' and (resid 175 through 253 )BC175 - 253172 - 237
88chain 'B' and (resid 254 through 325 )BC254 - 325238 - 309
99chain 'B' and (resid 326 through 428 )BC326 - 428310 - 412
1010chain 'C' and (resid 1 through 83 )CD1 - 831 - 83
1111chain 'C' and (resid 84 through 143 )CD84 - 14384 - 143
1212chain 'C' and (resid 144 through 226 )CD144 - 226144 - 226
1313chain 'C' and (resid 227 through 325 )CD227 - 325227 - 325
1414chain 'C' and (resid 326 through 421 )CD326 - 421326 - 421
1515chain 'C' and (resid 422 through 515 )CD422 - 515422 - 515
1616chain 'C' and (resid 516 through 554 )CD516 - 554516 - 554
1717chain 'D' and (resid 4 through 90 )DE4 - 901 - 87
1818chain 'D' and (resid 91 through 212 )DE91 - 21288 - 209
1919chain 'D' and (resid 213 through 253 )DE213 - 253210 - 237
2020chain 'D' and (resid 254 through 363 )DE254 - 363238 - 347
2121chain 'D' and (resid 364 through 428 )DE364 - 428348 - 412
2222chain 'E' and (resid 0 through 11 )EF0 - 11
2323chain 'E' and (resid 12 through 21 )EF12 - 21
2424chain 'E' and (resid 22 through 34 )EF22 - 34
2525chain 'F' and (resid 0 through 16 )FG0 - 16
2626chain 'F' and (resid 17 through 21 )FG17 - 21
2727chain 'F' and (resid 22 through 34 )FG22 - 34

+
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