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- PDB-6b2h: P38A/T216I mutant of the HIV-1 capsid protein -

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Basic information

Entry
Database: PDB / ID: 6b2h
TitleP38A/T216I mutant of the HIV-1 capsid protein
ComponentsHIV-1 capsid protein
KeywordsVIRAL PROTEIN / HIV-1 capsid protein / hexamer / P38A/T216I mutant
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral process / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell cytoplasm / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity ...viral budding via host ESCRT complex / viral process / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell cytoplasm / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane / cytoplasm
Similarity search - Function
Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain ...Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / 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
IODIDE ION / Gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsGres, A.T. / Kirby, K.A. / Sarafianos, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI120860 United States
CitationJournal: Nat Commun / Year: 2023
Title: Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization.
Authors: Gres, A.T. / Kirby, K.A. / McFadden, W.M. / Du, H. / Liu, D. / Xu, C. / Bryer, A.J. / Perilla, J.R. / Shi, J. / Aiken, C. / Fu, X. / Zhang, P. / Francis, A.C. / Melikyan, G.B. / Sarafianos, S.G.
History
DepositionSep 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_initial_refinement_model
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,59113
Polymers25,6161
Non-polymers97412
Water61334
1
A: HIV-1 capsid protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)159,54478
Polymers153,6996
Non-polymers5,84572
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area26350 Å2
ΔGint-415 kcal/mol
Surface area61780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.242, 92.242, 57.735
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

#1: Protein HIV-1 capsid protein


Mass: 25616.443 Da / Num. of mol.: 1 / Fragment: UNP residues 133-363 / Mutation: P38A, T216I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B6DRA0, UniProt: P12493*PLUS
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.56 % / Mosaicity: 0.1 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350, NaI, Sodium cacodylate, Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 2.6→46.8 Å / Num. obs: 8764 / % possible obs: 99.8 % / Redundancy: 9.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.024 / Rrim(I) all: 0.075 / Net I/σ(I): 15.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.6-2.719.30.80410370.7910.2730.8598.4
8.99-46.7990.0492300.9970.0180.05399.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.35 Å46.79 Å
Translation5.35 Å46.79 Å

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
Blu-Icedata collection
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
Aimless0.5.31data reduction
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XFX
Resolution: 2.6→46.8 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 34.12 / SU ML: 0.329 / SU R Cruickshank DPI: 0.6489 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.649 / ESU R Free: 0.295
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.241 521 5.9 %RANDOM
Rwork0.2003 ---
obs0.2029 8242 99.74 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 184.92 Å2 / Biso mean: 97.797 Å2 / Biso min: 58.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0.32 Å2-0 Å2
2---0.65 Å20 Å2
3---2.11 Å2
Refinement stepCycle: final / Resolution: 2.6→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1700 0 12 34 1746
Biso mean--115.92 76.52 -
Num. residues----219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191746
X-RAY DIFFRACTIONr_bond_other_d0.0020.021629
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.9582375
X-RAY DIFFRACTIONr_angle_other_deg0.92533797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8175221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54924.86574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7315303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7511510
X-RAY DIFFRACTIONr_chiral_restr0.0660.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211922
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02320
X-RAY DIFFRACTIONr_sphericity_free49.94154
X-RAY DIFFRACTIONr_sphericity_bonded49.2558
LS refinement shellResolution: 2.596→2.663 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 33 -
Rwork0.377 583 -
all-616 -
obs--97.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.5936-5.53691.540223.4889-7.74542.83940.1765-0.4988-0.04790.0936-0.5075-0.6745-0.35980.71110.3310.9161-0.3647-0.14821.36740.36360.48542.3179-11.843318.8621
26.1644.26391.877610.5844-13.89430.90571.685-0.079-0.74921.3219-0.32690.11480.17280.8614-1.35810.55390.13060.02730.4880.1140.5744-3.1877-11.308913.4235
37.5612-5.7542-3.723413.1168.451316.9583-0.03070.37791.1509-0.44520.0882-0.1929-1.59610.2468-0.05750.2683-0.00370.00020.40370.0820.6011-0.8295-13.4048-3.005
418.65475.2774.26051.50991.21310.9839-0.17850.3556-0.8428-0.15560.24-0.1638-0.13730.0409-0.06150.65680.13580.02920.40110.19680.74494.1731-20.274-9.5209
512.0328-0.12074.596815.1618-2.44056.4403-0.28210.66080.24330.15110.0075-0.4972-0.2298-0.18610.27460.2914-0.0491-0.0150.36220.02930.49786.2857-19.41960.4682
60.8491-0.83990.09795.92982.81467.7355-0.0292-0.04310.12450.2105-0.0927-0.1783-0.31450.170.12190.2919-0.02370.03840.36190.04410.4631-4.6031-22.99860.9832
70.9858-0.95752.16217.2228-6.891125.4498-0.2138-0.0602-0.37710.45990.0604-0.28340.67870.06720.15340.3806-0.00360.08960.33780.02410.4705-1.8605-37.88898.2715
80.5465-2.1331.028.4864-4.1032.0283-0.3063-0.1268-0.24021.09920.62550.7313-0.3544-0.2471-0.31920.86920.14060.14590.7116-0.00280.5184-10.7591-36.167828.1745
93.2582-1.6008-10.84012.12396.07437.53470.0013-0.36010.01210.58870.0683-0.0810.44630.5007-0.06960.5305-0.02440.08390.503-0.09790.4611-6.7784-31.652620.246
101.4401-2.7842-0.17786.6759-2.03544.7455-0.4359-0.22060.02250.88250.55530.0633-0.8191-0.4036-0.11940.64720.0333-0.00720.3639-0.07250.53-7.9688-24.488616.657
114.7996-0.28555.13680.9229-4.703826.99920.1485-1.23150.47170.108-0.25170.0229-0.01870.08390.10320.94890.1237-0.05530.4979-0.01020.48521.3636-25.815417.9278
1213.0834-1.2549-16.76512.68744.785825.4451-0.2247-0.4641-0.43790.19540.1296-0.39540.5120.7960.09510.32220.03750.0080.39950.10020.53384.4398-30.67611.2968
1324.6546-3.0928-13.10030.39091.68899.985-0.18230.7634-0.27320.0386-0.09070.06650.3821-1.34260.2730.51660.03950.08970.4533-0.00250.45512.8131-33.0465-13.8362
1417.4204-5.24980.42371.6155-0.43733.02070.36480.3314-0.517-0.1383-0.14320.169-0.08320.2784-0.22160.6272-0.07750.12370.5290.00620.39427.7133-25.1865-22.5515
158.86842.556-3.32635.8085-5.900311.2920.01060.17060.5413-0.3813-0.24660.069-0.28070.47850.2360.3580.03510.01940.32120.05540.365922.6013-24.5061-13.7703
1610.7472-5.41077.251516.8129-2.46894.99530.1271-0.1837-1.0894-0.19830.6431.93030.1703-0.0389-0.77010.36250.00260.1740.47180.0490.591515.3777-31.611-5.1209
1721.5586-4.015-9.99728.52180.937310.6334-0.2971-0.2783-0.0470.4741-0.1764-0.52210.01340.52210.47360.4148-0.0069-0.03060.30420.05830.387324.1872-35.4222-3.4972
184.32279.2246-3.021920.6166-7.65863.7-0.09080.2058-0.5226-0.828-0.1395-1.00360.84460.58520.23030.54230.35310.07040.58770.03020.535129.6247-32.6585-13.8663
1915.963-0.14841.41049.31653.23581.26090.00950.3249-0.5756-0.12230.0512-0.3902-0.0852-0.0162-0.06070.57630.16990.10330.54660.0590.420838.0937-28.9938-15.6024
208.09750.0488-7.24677.7218-1.379819.38880.23460.17360.5437-0.73890.3625-0.2275-0.05871.6039-0.59710.27510.01240.00480.47880.04310.514735.2744-20.3709-12.2814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 8
2X-RAY DIFFRACTION2A9 - 17
3X-RAY DIFFRACTION3A18 - 27
4X-RAY DIFFRACTION4A28 - 34
5X-RAY DIFFRACTION5A35 - 44
6X-RAY DIFFRACTION6A45 - 67
7X-RAY DIFFRACTION7A68 - 85
8X-RAY DIFFRACTION8A86 - 93
9X-RAY DIFFRACTION9A94 - 104
10X-RAY DIFFRACTION10A105 - 118
11X-RAY DIFFRACTION11A119 - 131
12X-RAY DIFFRACTION12A132 - 142
13X-RAY DIFFRACTION13A143 - 153
14X-RAY DIFFRACTION14A154 - 161
15X-RAY DIFFRACTION15A162 - 172
16X-RAY DIFFRACTION16A173 - 178
17X-RAY DIFFRACTION17A179 - 185
18X-RAY DIFFRACTION18A186 - 195
19X-RAY DIFFRACTION19A196 - 209
20X-RAY DIFFRACTION20A210 - 221

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