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- PDB-8d3b: Hexameric HIV-1 (M-group) Q50Y/R120 mutant -

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Basic information

Entry
Database: PDB / ID: 8d3b
TitleHexameric HIV-1 (M-group) Q50Y/R120 mutant
ComponentsCapsid protein p24
KeywordsVIRAL PROTEIN / Capsid
Function / homology
Function and homology information


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 / ATP 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 knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsJacques, D.A. / Govasli, M.L. / Pinotsis, N. / 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
DepositionJun 1, 2022Deposition 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)153,9216
Polymers153,9216
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13680 Å2
ΔGint-101 kcal/mol
Surface area55590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.920, 157.310, 120.400
Angle α, β, γ (deg.)90.000, 107.280, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROVALVAL(chain 'A' and (resid 1 through 25 or resid 27...AA1 - 241 - 24
12VALVALPROPRO(chain 'A' and (resid 1 through 25 or resid 27...AA27 - 3427 - 34
13METMETARGARG(chain 'A' and (resid 1 through 25 or resid 27...AA39 - 8239 - 82
14METMETTRPTRP(chain 'A' and (resid 1 through 25 or resid 27...AA96 - 11796 - 117
15PROPROTHRTHR(chain 'A' and (resid 1 through 25 or resid 27...AA124 - 149124 - 149
16LEULEUGLNGLN(chain 'A' and (resid 1 through 25 or resid 27...AA152 - 156152 - 156
17LYSLYSALAALA(chain 'A' and (resid 1 through 25 or resid 27...AA159 - 175159 - 175
18THRTHRALAALA(chain 'A' and (resid 1 through 25 or resid 27...AA189 - 195189 - 195
19LYSLYSGLUGLU(chain 'A' and (resid 1 through 25 or resid 27...AA200 - 213200 - 213
110METMETCYSCYS(chain 'A' and (resid 1 through 25 or resid 27...AA216 - 219216 - 219
21PROPROVALVAL(chain 'B' and (resid 1 through 25 or resid 27...BB1 - 241 - 24
22VALVALPROPRO(chain 'B' and (resid 1 through 25 or resid 27...BB27 - 3427 - 34
23METMETARGARG(chain 'B' and (resid 1 through 25 or resid 27...BB39 - 8239 - 82
24METMETTRPTRP(chain 'B' and (resid 1 through 25 or resid 27...BB96 - 11796 - 117
25PROPROTHRTHR(chain 'B' and (resid 1 through 25 or resid 27...BB124 - 149124 - 149
26LEULEUGLNGLN(chain 'B' and (resid 1 through 25 or resid 27...BB152 - 156152 - 156
27LYSLYSALAALA(chain 'B' and (resid 1 through 25 or resid 27...BB159 - 175159 - 175
28THRTHRALAALA(chain 'B' and (resid 1 through 25 or resid 27...BB189 - 195189 - 195
29LYSLYSGLUGLU(chain 'B' and (resid 1 through 25 or resid 27...BB200 - 213200 - 213
210METMETCYSCYS(chain 'B' and (resid 1 through 25 or resid 27...BB216 - 219216 - 219
31PROPROVALVAL(chain 'C' and (resid 1 through 25 or resid 27...CC1 - 241 - 24
32VALVALPROPRO(chain 'C' and (resid 1 through 25 or resid 27...CC27 - 3427 - 34
33METMETARGARG(chain 'C' and (resid 1 through 25 or resid 27...CC39 - 8239 - 82
34METMETTRPTRP(chain 'C' and (resid 1 through 25 or resid 27...CC96 - 11796 - 117
35PROPROTHRTHR(chain 'C' and (resid 1 through 25 or resid 27...CC124 - 149124 - 149
36LEULEUGLNGLN(chain 'C' and (resid 1 through 25 or resid 27...CC152 - 156152 - 156
37LYSLYSALAALA(chain 'C' and (resid 1 through 25 or resid 27...CC159 - 175159 - 175
38THRTHRALAALA(chain 'C' and (resid 1 through 25 or resid 27...CC189 - 195189 - 195
39LYSLYSGLUGLU(chain 'C' and (resid 1 through 25 or resid 27...CC200 - 213200 - 213
310METMETCYSCYS(chain 'C' and (resid 1 through 25 or resid 27...CC216 - 219216 - 219
41PROPROVALVAL(chain 'D' and (resid 1 through 25 or resid 27...DD1 - 241 - 24
42VALVALPROPRO(chain 'D' and (resid 1 through 25 or resid 27...DD27 - 3427 - 34
43METMETARGARG(chain 'D' and (resid 1 through 25 or resid 27...DD39 - 8239 - 82
44METMETTRPTRP(chain 'D' and (resid 1 through 25 or resid 27...DD96 - 11796 - 117
45PROPROTHRTHR(chain 'D' and (resid 1 through 25 or resid 27...DD124 - 149124 - 149
46LEULEUGLNGLN(chain 'D' and (resid 1 through 25 or resid 27...DD152 - 156152 - 156
47LYSLYSALAALA(chain 'D' and (resid 1 through 25 or resid 27...DD159 - 175159 - 175
48THRTHRALAALA(chain 'D' and (resid 1 through 25 or resid 27...DD189 - 195189 - 195
49LYSLYSGLUGLU(chain 'D' and (resid 1 through 25 or resid 27...DD200 - 213200 - 213
410METMETCYSCYS(chain 'D' and (resid 1 through 25 or resid 27...DD216 - 219216 - 219
51PROPROVALVAL(chain 'E' and (resid 1 through 25 or resid 27...EE1 - 241 - 24
52VALVALPROPRO(chain 'E' and (resid 1 through 25 or resid 27...EE27 - 3427 - 34
53METMETARGARG(chain 'E' and (resid 1 through 25 or resid 27...EE39 - 8239 - 82
54METMETTRPTRP(chain 'E' and (resid 1 through 25 or resid 27...EE96 - 11796 - 117
55PROPROTHRTHR(chain 'E' and (resid 1 through 25 or resid 27...EE124 - 149124 - 149
56LEULEUGLNGLN(chain 'E' and (resid 1 through 25 or resid 27...EE152 - 156152 - 156
57LYSLYSALAALA(chain 'E' and (resid 1 through 25 or resid 27...EE159 - 175159 - 175
58THRTHRALAALA(chain 'E' and (resid 1 through 25 or resid 27...EE189 - 195189 - 195
59LYSLYSGLUGLU(chain 'E' and (resid 1 through 25 or resid 27...EE200 - 213200 - 213
510METMETCYSCYS(chain 'E' and (resid 1 through 25 or resid 27...EE216 - 219216 - 219
61PROPROVALVAL(chain 'F' and (resid 1 through 25 or resid 27...FF1 - 241 - 24
62VALVALPROPRO(chain 'F' and (resid 1 through 25 or resid 27...FF27 - 3427 - 34
63METMETARGARG(chain 'F' and (resid 1 through 25 or resid 27...FF39 - 8239 - 82
64METMETTRPTRP(chain 'F' and (resid 1 through 25 or resid 27...FF96 - 11796 - 117
65PROPROTHRTHR(chain 'F' and (resid 1 through 25 or resid 27...FF124 - 149124 - 149
66LEULEUGLNGLN(chain 'F' and (resid 1 through 25 or resid 27...FF152 - 156152 - 156
67LYSLYSALAALA(chain 'F' and (resid 1 through 25 or resid 27...FF159 - 175159 - 175
68THRTHRALAALA(chain 'F' and (resid 1 through 25 or resid 27...FF189 - 195189 - 195
69LYSLYSGLUGLU(chain 'F' and (resid 1 through 25 or resid 27...FF200 - 213200 - 213
610METMETCYSCYS(chain 'F' and (resid 1 through 25 or resid 27...FF216 - 219216 - 219

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Components

#1: Protein
Capsid protein p24


Mass: 25653.512 Da / Num. of mol.: 6 / Mutation: Q50Y, R120(insertion), A14C, E45C, W185A, M186A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B6DRA0
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG550MME, 0.1M TRIS (pH 8.0), 0.15M KSCN, 10mM ATP, 3% EtOH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.29→76.01 Å / Num. obs: 24392 / % possible obs: 99.7 % / Redundancy: 3.3 % / CC1/2: 0.976 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.123 / Rrim(I) all: 0.229 / Net I/σ(I): 5 / Num. measured all: 80466 / Scaling rejects: 71
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
3.29-3.523.20.5951393143660.8130.3820.71299
9.32-76.013.30.06361811040.9780.0410.07312.499.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.58 Å76.01 Å
Translation7.58 Å76.01 Å

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Processing

Software
NameVersionClassification
Aimless0.5.7data scaling
PHASER2.5.7phasing
PHENIX1.14refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7T13

7t13


Resolution: 3.3→64.92 Å / SU ML: 0.4288 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.0989 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2748 1222 5.03 %
Rwork0.239 23049 -
obs0.2408 24271 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.27 Å2
Refinement stepCycle: LAST / Resolution: 3.3→64.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9029 0 0 0 9029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00199277
X-RAY DIFFRACTIONf_angle_d0.394812612
X-RAY DIFFRACTIONf_chiral_restr0.03431441
X-RAY DIFFRACTIONf_plane_restr0.0041610
X-RAY DIFFRACTIONf_dihedral_angle_d1.31337812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.430.31061510.27712553X-RAY DIFFRACTION99.82
3.43-3.590.30881430.25272545X-RAY DIFFRACTION99.7
3.59-3.780.30441250.25972554X-RAY DIFFRACTION99.67
3.78-4.010.28381150.23432560X-RAY DIFFRACTION99.37
4.01-4.320.29611300.23592565X-RAY DIFFRACTION99.41
4.32-4.760.25291160.22812561X-RAY DIFFRACTION99.59
4.76-5.450.28421220.22282570X-RAY DIFFRACTION100
5.45-6.860.30311450.25212580X-RAY DIFFRACTION100
6.86-64.920.22231750.22272561X-RAY DIFFRACTION99.38

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