[English] 日本語
Yorodumi
- PDB-7t12: Hexameric HIV-1 (O-group) CA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7t12
TitleHexameric HIV-1 (O-group) CA
ComponentsCapsid protein p24
KeywordsVIRAL PROTEIN / Capsid
Function / homology
Function and homology information


viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane
Similarity search - Function
Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal ...Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHIV-1 O_MVP5180 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsJacques, D.A. / James, L.C.
Funding support Australia, United Kingdom, European Union, 6items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP180101384 Australia
National Health and Medical Research Council (NHMRC, Australia)GNT1158338 Australia
Wellcome Trust214344/Z/18/Z United Kingdom
Wellcome Trust108183 United Kingdom
Wellcome Trust220863 United Kingdom
European Research Council (ERC)339223European Union
CitationJournal: Nat Microbiol / Year: 2022
Title: Evasion of cGAS and TRIM5 defines pandemic HIV.
Authors: Zuliani-Alvarez, L. / Govasli, M.L. / Rasaiyaah, J. / Monit, C. / Perry, S.O. / Sumner, R.P. / McAlpine-Scott, S. / Dickson, C. / Rifat Faysal, K.M. / Hilditch, L. / Miles, R.J. / Bibollet- ...Authors: Zuliani-Alvarez, L. / Govasli, M.L. / Rasaiyaah, J. / Monit, C. / Perry, S.O. / Sumner, R.P. / McAlpine-Scott, S. / Dickson, C. / Rifat Faysal, K.M. / Hilditch, L. / Miles, R.J. / Bibollet-Ruche, F. / Hahn, B.H. / Boecking, T. / Pinotsis, N. / James, L.C. / Jacques, D.A. / Towers, G.J.
History
DepositionDec 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein p24
B: Capsid protein p24
C: Capsid protein p24
D: Capsid protein p24
E: Capsid protein p24
F: Capsid protein p24
G: Capsid protein p24
H: Capsid protein p24
I: Capsid protein p24
J: Capsid protein p24
K: Capsid protein p24
L: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)305,65612
Polymers305,65612
Non-polymers00
Water00
1
A: Capsid protein p24
B: Capsid protein p24
C: Capsid protein p24
D: Capsid protein p24
E: Capsid protein p24
F: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)152,8286
Polymers152,8286
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13160 Å2
ΔGint-95 kcal/mol
Surface area58540 Å2
MethodPISA
2
G: Capsid protein p24
H: Capsid protein p24
I: Capsid protein p24
J: Capsid protein p24
K: Capsid protein p24
L: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)152,8286
Polymers152,8286
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13320 Å2
ΔGint-101 kcal/mol
Surface area57300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.200, 151.730, 120.420
Angle α, β, γ (deg.)90.000, 105.030, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 37 or resid 39...
21(chain B and (resid 1 through 37 or resid 39...
31(chain C and (resid 1 through 37 or resid 39...
41(chain D and (resid 1 through 37 or resid 39...
51(chain E and (resid 1 through 37 or resid 39...
61(chain F and (resid 1 through 37 or resid 39...
71(chain G and (resid 1 through 37 or resid 39...
81(chain H and (resid 1 through 37 or resid 39...
91(chain I and (resid 1 through 37 or resid 39...
101(chain J and (resid 1 through 37 or resid 39...
111(chain K and (resid 1 through 37 or resid 39...
121(chain L and (resid 1 through 37 or resid 39...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 37 or resid 39...A1 - 37
121(chain A and (resid 1 through 37 or resid 39...A39 - 85
131(chain A and (resid 1 through 37 or resid 39...A1 - 220
141(chain A and (resid 1 through 37 or resid 39...A1 - 220
151(chain A and (resid 1 through 37 or resid 39...A1
161(chain A and (resid 1 through 37 or resid 39...A1 - 220
171(chain A and (resid 1 through 37 or resid 39...A1 - 220
181(chain A and (resid 1 through 37 or resid 39...A1 - 220
191(chain A and (resid 1 through 37 or resid 39...A1 - 220
1101(chain A and (resid 1 through 37 or resid 39...A1 - 220
211(chain B and (resid 1 through 37 or resid 39...B1 - 37
221(chain B and (resid 1 through 37 or resid 39...B39 - 85
231(chain B and (resid 1 through 37 or resid 39...B1 - 220
241(chain B and (resid 1 through 37 or resid 39...B1 - 220
251(chain B and (resid 1 through 37 or resid 39...B12
261(chain B and (resid 1 through 37 or resid 39...B1 - 220
271(chain B and (resid 1 through 37 or resid 39...B1 - 220
281(chain B and (resid 1 through 37 or resid 39...B1 - 220
291(chain B and (resid 1 through 37 or resid 39...B1 - 220
311(chain C and (resid 1 through 37 or resid 39...C1 - 37
321(chain C and (resid 1 through 37 or resid 39...C39 - 85
331(chain C and (resid 1 through 37 or resid 39...C97 - 119
341(chain C and (resid 1 through 37 or resid 39...C120
351(chain C and (resid 1 through 37 or resid 39...C1 - 220
361(chain C and (resid 1 through 37 or resid 39...C1 - 220
371(chain C and (resid 1 through 37 or resid 39...C1 - 220
381(chain C and (resid 1 through 37 or resid 39...C1 - 220
411(chain D and (resid 1 through 37 or resid 39...D1 - 37
421(chain D and (resid 1 through 37 or resid 39...D39 - 85
431(chain D and (resid 1 through 37 or resid 39...D97 - 150
441(chain D and (resid 1 through 37 or resid 39...D1 - 220
451(chain D and (resid 1 through 37 or resid 39...D176 - 189
461(chain D and (resid 1 through 37 or resid 39...D1 - 220
471(chain D and (resid 1 through 37 or resid 39...D1 - 220
481(chain D and (resid 1 through 37 or resid 39...D1 - 220
491(chain D and (resid 1 through 37 or resid 39...D1 - 220
4101(chain D and (resid 1 through 37 or resid 39...D1 - 220
511(chain E and (resid 1 through 37 or resid 39...E1 - 37
521(chain E and (resid 1 through 37 or resid 39...E39 - 85
531(chain E and (resid 1 through 37 or resid 39...E97 - 119
541(chain E and (resid 1 through 37 or resid 39...E120
551(chain E and (resid 1 through 37 or resid 39...E1 - 220
561(chain E and (resid 1 through 37 or resid 39...E1 - 220
571(chain E and (resid 1 through 37 or resid 39...E1 - 220
581(chain E and (resid 1 through 37 or resid 39...E1 - 220
611(chain F and (resid 1 through 37 or resid 39...F1 - 37
621(chain F and (resid 1 through 37 or resid 39...F39 - 85
631(chain F and (resid 1 through 37 or resid 39...F97 - 119
641(chain F and (resid 1 through 37 or resid 39...F120
651(chain F and (resid 1 through 37 or resid 39...F1 - 220
661(chain F and (resid 1 through 37 or resid 39...F1 - 220
671(chain F and (resid 1 through 37 or resid 39...F1 - 220
681(chain F and (resid 1 through 37 or resid 39...F1 - 220
711(chain G and (resid 1 through 37 or resid 39...G1 - 37
721(chain G and (resid 1 through 37 or resid 39...G39 - 85
731(chain G and (resid 1 through 37 or resid 39...G1 - 220
741(chain G and (resid 1 through 37 or resid 39...G1 - 220
751(chain G and (resid 1 through 37 or resid 39...G120
761(chain G and (resid 1 through 37 or resid 39...G1 - 220
771(chain G and (resid 1 through 37 or resid 39...G1 - 220
781(chain G and (resid 1 through 37 or resid 39...G1 - 220
791(chain G and (resid 1 through 37 or resid 39...G1 - 220
811(chain H and (resid 1 through 37 or resid 39...H1 - 37
821(chain H and (resid 1 through 37 or resid 39...H39 - 85
831(chain H and (resid 1 through 37 or resid 39...H97 - 11
841(chain H and (resid 1 through 37 or resid 39...H1 - 220
851(chain H and (resid 1 through 37 or resid 39...H1 - 220
861(chain H and (resid 1 through 37 or resid 39...H1 - 220
871(chain H and (resid 1 through 37 or resid 39...H1 - 220
881(chain H and (resid 1 through 37 or resid 39...H1 - 220
911(chain I and (resid 1 through 37 or resid 39...I1 - 37
921(chain I and (resid 1 through 37 or resid 39...I39 - 85
931(chain I and (resid 1 through 37 or resid 39...I97 - 119
941(chain I and (resid 1 through 37 or resid 39...I120
951(chain I and (resid 1 through 37 or resid 39...I1 - 220
961(chain I and (resid 1 through 37 or resid 39...I1 - 220
971(chain I and (resid 1 through 37 or resid 39...I1 - 220
981(chain I and (resid 1 through 37 or resid 39...I1 - 220
1011(chain J and (resid 1 through 37 or resid 39...J1 - 37
1021(chain J and (resid 1 through 37 or resid 39...J39 - 85
1031(chain J and (resid 1 through 37 or resid 39...J1 - 220
1041(chain J and (resid 1 through 37 or resid 39...J1 - 220
1051(chain J and (resid 1 through 37 or resid 39...J152
1061(chain J and (resid 1 through 37 or resid 39...J159 - 175
1071(chain J and (resid 1 through 37 or resid 39...J0
1081(chain J and (resid 1 through 37 or resid 39...J1 - 220
1091(chain J and (resid 1 through 37 or resid 39...J1 - 220
10101(chain J and (resid 1 through 37 or resid 39...J1 - 220
10111(chain J and (resid 1 through 37 or resid 39...J1 - 220
1111(chain K and (resid 1 through 37 or resid 39...K1 - 37
1121(chain K and (resid 1 through 37 or resid 39...K39 - 150
1131(chain K and (resid 1 through 37 or resid 39...K152 - 57
1141(chain K and (resid 1 through 37 or resid 39...K1 - 220
1151(chain K and (resid 1 through 37 or resid 39...K1 - 220
1161(chain K and (resid 1 through 37 or resid 39...K1 - 220
1171(chain K and (resid 1 through 37 or resid 39...K1 - 220
1181(chain K and (resid 1 through 37 or resid 39...K1 - 220
1191(chain K and (resid 1 through 37 or resid 39...K1 - 220
1211(chain L and (resid 1 through 37 or resid 39...L1 - 37
1221(chain L and (resid 1 through 37 or resid 39...L39 - 85
1231(chain L and (resid 1 through 37 or resid 39...L97 - 119
1241(chain L and (resid 1 through 37 or resid 39...L120
1251(chain L and (resid 1 through 37 or resid 39...L1 - 220
1261(chain L and (resid 1 through 37 or resid 39...L1 - 220
1271(chain L and (resid 1 through 37 or resid 39...L1 - 220
1281(chain L and (resid 1 through 37 or resid 39...L1 - 220

-
Components

#1: Protein
Capsid protein p24 / CA


Mass: 25471.320 Da / Num. of mol.: 12 / Mutation: A14C, E45C, W185A, M186A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 O_MVP5180 (virus) / Strain: isolate MVP5180 / Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: Q79665
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Crystallant: 10% (w/v) PEG 6000, 100 mM HEPES (pH 7.0), 100 mM Glycine. Crystals grew in 2 ul protein (40 mg/ml) + 2 ul crystallant. Cryoprotected in 40% (w/v) glucose

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 3→75.86 Å / Num. obs: 59020 / % possible obs: 97.7 % / Redundancy: 5 % / CC1/2: 0.908 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.088 / Rrim(I) all: 0.193 / Net I/σ(I): 5.9 / Num. measured all: 295052 / Scaling rejects: 3631
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3-3.084.71.2082130045800.2820.6261.3691.897.5
13.08-75.865.10.11438327520.9750.0560.1299.298

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å75.86 Å
Translation3 Å75.86 Å

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.6.3data scaling
PHASER2.8.2phasing
PHENIX1.14refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H47

3h47


Resolution: 3→75.86 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2586 2934 5.01 %
Rwork0.2144 55643 -
obs0.2166 58577 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 241.15 Å2 / Biso mean: 95.3919 Å2 / Biso min: 27.95 Å2
Refinement stepCycle: final / Resolution: 3→75.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18717 0 0 0 18717
Num. residues----2419
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6504X-RAY DIFFRACTION1.955TORSIONAL
12B6504X-RAY DIFFRACTION1.955TORSIONAL
13C6504X-RAY DIFFRACTION1.955TORSIONAL
14D6504X-RAY DIFFRACTION1.955TORSIONAL
15E6504X-RAY DIFFRACTION1.955TORSIONAL
16F6504X-RAY DIFFRACTION1.955TORSIONAL
17G6504X-RAY DIFFRACTION1.955TORSIONAL
18H6504X-RAY DIFFRACTION1.955TORSIONAL
19I6504X-RAY DIFFRACTION1.955TORSIONAL
110J6504X-RAY DIFFRACTION1.955TORSIONAL
111K6504X-RAY DIFFRACTION1.955TORSIONAL
112L6504X-RAY DIFFRACTION1.955TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3-3.04920.37281320.3118262898
3.0492-3.10180.30561560.3035264397
3.1018-3.15820.37461320.2714265898
3.1582-3.2190.3261560.2591271498
3.219-3.28470.31921460.2646262998
3.2847-3.35610.31121390.2609273498
3.3561-3.43420.44161240.3481260296
3.4342-3.520.43851320.3613259495
3.52-3.61520.30511240.2526268198
3.6152-3.72160.30931370.3274249692
3.7216-3.84170.29241590.2279262796
3.8417-3.9790.32591300.2996251491
3.979-4.13830.27231560.1815266598
4.1383-4.32660.21651370.1708265197
4.3266-4.55470.19851390.1545266898
4.5547-4.840.19941280.1473272698
4.84-5.21370.21981230.1598267697
5.2137-5.73820.23691520.1757269799
5.7382-6.56810.24591440.1951267597
6.5681-8.27350.22321350.1873270297
8.2735-75.860.2021530.1854266395
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)
14.78630.34960.39345.9074-0.95788.4301-0.05830.5193-0.439-0.36660.00170.61070.85120.03760.050.3904-0.06990.02140.36660.00850.601711.178-8.867110.055
26.13480.3038-2.76534.983-0.14129.4669-0.0613-0.9711-0.07630.8392-0.1222-0.40770.15330.9793-0.19040.5117-0.0508-0.03390.627-0.03990.3228-2.562-6.348142.182
33.77260.6313-1.48945.2781-0.13937.217-0.10380.422-0.3018-0.0615-0.21470.18830.3675-0.41850.22190.2797-0.0137-0.02330.4305-0.0530.4215-12.149-10.65118.413
43.3629-3.2687-1.97927.97882.99546.92130.0193-0.6209-0.01260.4534-0.10450.88280.004-0.96730.1350.52160.17150.17480.9471-0.04450.6278-34.50812.823134.782
56.93361.1661.05436.92871.3576.99710.03580.30320.1921-0.1767-0.010.66920.2317-0.2319-00.3370.02490.01660.35910.07570.4426-29.7135.656109.57
61.0178-1.2676-0.75914.61431.75354.93770.27230.14431.29051.19090.35840.8776-1.592-0.0872-0.39730.9190.0870.40410.57560.10231.7277-27.80243.641114.375
75.45120.22112.55325.22490.11287.14540.27330.61580.3382-0.5621-0.02391.00270.2127-0.2378-0.14550.36860.0676-0.00680.57370.12310.7499-23.74225.78894.553
84.79070.75452.4379.81231.99685.0459-0.45980.0022-0.1066-0.02470.781-1.7901-0.88270.7522-0.19740.5589-0.14370.18120.5425-0.1240.79154.50649.81497.276
96.0702-0.25671.07685.34562.48947.59020.02770.2556-0.1089-0.60390.03750.1621-0.0212-0.2021-0.09680.45550.0010.06790.3518-0.01550.4314-0.31626.30184.763
107.98553.90824.70156.6060.23176.99460.3165-0.9925-0.73190.80780.0129-1.8791-0.21830.6107-0.15560.6779-0.2017-0.05770.6680.04831.293233.12727.287102.412
114.4966-1.15130.92766.2277-0.96875.36870.30220.376-0.0413-0.9848-0.6231-0.58960.78620.25960.33080.90740.06560.23220.34550.06020.76516.9158.33491.507
125.47091.4731-0.72681.74521.3815.32280.0081-0.96980.56680.28830.1009-0.2604-0.6892.011-0.10120.3873-0.1533-0.0871.1394-0.03290.935229.3970.672126.011
133.88862.89052.18129.1362-0.08275.30370.02060.05730.40060.78060.02150.2792-0.08120.62340.08980.44690.04650.06940.617-0.07980.3406-20.882-32.35584.57
146.5991-3.34780.9547.8925-0.97970.88230.23670.0306-2.6284-0.0588-0.10190.84380.42520.1508-0.09390.65480.05160.10160.5569-0.03581.0946-8.393-68.08679.615
155.77230.46180.68224.38560.81615.6046-0.5149-0.94050.42960.27220.21210.0605-0.09730.00750.31270.41260.183-0.12340.7412-0.12420.54191.951-44.67586.979
162.0612-2.2704-0.46996.77312.12744.9735-1.29321.5932-2.3831-0.51090.3308-1.16660.9296-0.33520.57460.78160.11110.40391.1224-0.38891.109123.928-61.70662.772
176.23751.12772.00276.0220.75278.4142-0.54120.4881.5140.03010.15470.457-0.16570.10360.26610.46280.0918-0.01820.60520.09270.587521.045-36.46572.64
183.7379-1.34242.17263.4153.67688.20130.1427-0.291-0.5099-1.2024-0.1247-0.04990.38911.02070.05611.21530.25040.24521.1330.22380.608223.4-35.67535.53
193.91260.78882.79838.9204-1.23248.2725-0.3220.1160.19150.41910.48150.5985-0.01240.0751-0.12650.34630.19620.08270.74260.10880.530717.31-18.6355.692
207.5480.9514.76691.03381.50867.0459-1.0751.39430.0972-0.5816-0.26210.4787-1.48520.49740.17070.93810.0089-0.5540.97440.21770.9393-5.128-13.93127.944
213.8255-1.6932-3.08835.22934.3078.1595-0.1539-0.8703-0.4848-0.0714-0.16080.3986-0.81780.8050.17630.6254-0.109-0.19410.79280.24140.7778-5.527-8.20453.61
228.07793.45920.03775.575-0.28592.8571-0.26930.22660.3504-0.5649-0.3430.9348-0.2036-1.0290.54920.62490.1535-0.25141.0512-0.33980.7843-39.061-21.60145.628
234.92892.24452.58415.88480.33597.1108-0.5543-0.55230.53190.4525-0.6124-0.0537-1.3355-0.49350.8090.68680.1644-0.34220.888-0.1540.6787-25.088-15.61867.403
242.00121.8711-1.27618.5146-2.29962.5876-0.1561-0.1928-0.4165-1.39890.43020.86732.1386-2.4659-0.30581.2339-0.7138-0.03431.64680.14960.6658-39.241-48.95372.578
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:143 )A1 - 143
2X-RAY DIFFRACTION2( CHAIN A AND RESID 144:220 )A144 - 220
3X-RAY DIFFRACTION3( CHAIN B AND RESID 1:143 )B1 - 143
4X-RAY DIFFRACTION4( CHAIN B AND RESID 144:220 )B144 - 220
5X-RAY DIFFRACTION5( CHAIN C AND RESID 1:143 )C1 - 143
6X-RAY DIFFRACTION6( CHAIN C AND RESID 144:220 )C144 - 220
7X-RAY DIFFRACTION7( CHAIN D AND RESID 1:143 )D1 - 143
8X-RAY DIFFRACTION8( CHAIN D AND RESID 144:220 )D144 - 220
9X-RAY DIFFRACTION9( CHAIN E AND RESID 1:143 )E1 - 143
10X-RAY DIFFRACTION10( CHAIN E AND RESID 144:220 )E144 - 220
11X-RAY DIFFRACTION11( CHAIN F AND RESID 1:143 )F1 - 143
12X-RAY DIFFRACTION12( CHAIN F AND RESID 144:220 )F144 - 220
13X-RAY DIFFRACTION13( CHAIN G AND RESID 1:143 )G1 - 143
14X-RAY DIFFRACTION14( CHAIN G AND RESID 144:220 )G144 - 220
15X-RAY DIFFRACTION15( CHAIN H AND RESID 1:143 )H1 - 143
16X-RAY DIFFRACTION16( CHAIN H AND RESID 144:220 )H144 - 220
17X-RAY DIFFRACTION17( CHAIN I AND RESID 1:143 )I1 - 143
18X-RAY DIFFRACTION18( CHAIN I AND RESID 144:220 )I144 - 220
19X-RAY DIFFRACTION19( CHAIN J AND RESID 1:143 )J1 - 143
20X-RAY DIFFRACTION20( CHAIN J AND RESID 144:220 )J144 - 220
21X-RAY DIFFRACTION21( CHAIN K AND RESID 1:143 )K1 - 143
22X-RAY DIFFRACTION22( CHAIN K AND RESID 144:220 )K144 - 220
23X-RAY DIFFRACTION23( CHAIN L AND RESID 1:143 )L1 - 143
24X-RAY DIFFRACTION24( CHAIN L AND RESID 144:220 )L144 - 220

+
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