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- PDB-7rmm: Structure of N74D mutant of disulfide stabilized HIV-1 CA hexamer -

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Basic information

Entry
Database: PDB / ID: 7rmm
TitleStructure of N74D mutant of disulfide stabilized HIV-1 CA hexamer
ComponentsCAPSID PROTEIN P24
KeywordsVIRAL PROTEIN / inhibitor
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
IODIDE ION / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsBester, S.M. / Kvaratskhelia, M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32 AI150547 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI150472 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI062520 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI143649 United States
CitationJournal: Mbio / Year: 2022
Title: Structural and Mechanistic Bases of Viral Resistance to HIV-1 Capsid Inhibitor Lenacapavir.
Authors: Bester, S.M. / Adu-Ampratwum, D. / Annamalai, A.S. / Wei, G. / Briganti, L. / Murphy, B.C. / Haney, R. / Fuchs, J.R. / Kvaratskhelia, M.
History
DepositionJul 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 2.0Aug 10, 2022Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Oct 19, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Nov 9, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 2.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAPSID PROTEIN P24
B: CAPSID PROTEIN P24
C: CAPSID PROTEIN P24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,75126
Polymers76,3873
Non-polymers1,36423
Water6,521362
1
A: CAPSID PROTEIN P24
B: CAPSID PROTEIN P24
hetero molecules

A: CAPSID PROTEIN P24
B: CAPSID PROTEIN P24
hetero molecules

A: CAPSID PROTEIN P24
B: CAPSID PROTEIN P24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,57354
Polymers152,7746
Non-polymers2,79948
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
2
C: CAPSID PROTEIN P24
hetero molecules

C: CAPSID PROTEIN P24
hetero molecules

C: CAPSID PROTEIN P24
hetero molecules

C: CAPSID PROTEIN P24
hetero molecules

C: CAPSID PROTEIN P24
hetero molecules

C: CAPSID PROTEIN P24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,36048
Polymers152,7746
Non-polymers2,58642
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
Unit cell
Length a, b, c (Å)157.360, 157.360, 56.575
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Space group name HallP6
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-440-

HOH

21B-523-

HOH

31B-532-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 5 or resid 10...
d_2ens_1(chain "B" and (resid 1 through 5 or resid 10...
d_3ens_1(chain "C" and (resid 1 through 17 or resid 19...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROASNA1 - 5
d_12ens_1METPROA10 - 17
d_13ens_1THRLEUA19 - 69
d_14ens_1GLUPROA72 - 86
d_15ens_1ARGPROA94 - 96
d_16ens_1GLYLYSA98 - 128
d_17ens_1TRPILEA131 - 151
d_18ens_1GLNGLNA153 - 174
d_19ens_1LEUVALA187 - 189
d_110ens_1ASNASPA191 - 195
d_111ens_1LYSLEUA198 - 210
d_112ens_1GLUGLNA212 - 218
d_21ens_1PROASNB1 - 5
d_22ens_1METPROB10 - 17
d_23ens_1THRLEUB19 - 69
d_24ens_1GLUPROB71 - 85
d_25ens_1ARGPROB91 - 93
d_26ens_1GLYLYSB95 - 125
d_27ens_1TRPILEB127 - 147
d_28ens_1GLNGLNB149 - 170
d_29ens_1LEUVALB183 - 185
d_210ens_1ASNASPB187 - 191
d_211ens_1LYSLEUB193 - 205
d_212ens_1GLUGLNB208 - 214
d_31ens_1PROPROC1 - 13
d_32ens_1THRLEUC15 - 65
d_33ens_1GLUPROC67 - 81
d_34ens_1ARGPROC87 - 89
d_35ens_1GLYLYSC91 - 121
d_36ens_1TRPILEC123 - 143
d_37ens_1GLNVALC145 - 169
d_38ens_1ASNASPC171 - 175
d_39ens_1LYSLEUC177 - 189
d_310ens_1GLUGLNC191 - 197

NCS oper:
IDCodeMatrixVector
1given(-0.999938761071, -0.00646738494596, -0.00898036965449), (0.00649519914508, -0.999974188748, -0.00307151848388), (-0.0089602731675, -0.00312965967668, 0.999954958353)156.96638019, -91.4514350634, 0.597149390724
2given(0.0265710476014, -0.999618468982, 0.00754293705275), (-0.999637874682, -0.0266021630137, -0.00405517252367), (0.00425428379065, -0.00743245538212, -0.999963329166)-47.4526180669, 77.4920889054, 27.4969299067

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Components

#1: Protein CAPSID PROTEIN P24


Mass: 25462.256 Da / Num. of mol.: 3 / Mutation: A14C, E45C, N74D, W184A, M185A
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
#2: Chemical
ChemComp-IOD / IODIDE ION


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


Mass: 35.453 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M NaI, 5% peg 3350, 6% glycerol, 0.1M sodium cacodylate trihydrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→45.43 Å / Num. obs: 56827 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 29.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Net I/σ(I): 15.8
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 10.2 % / Rmerge(I) obs: 1.308 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4002 / CC1/2: 0.639 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VKV

6vkv


Resolution: 1.97→45.43 Å / SU ML: 0.2559 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.704
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2465 2788 4.91 %
Rwork0.2178 53993 -
obs0.2192 56781 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.32 Å2
Refinement stepCycle: LAST / Resolution: 1.97→45.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4823 0 23 362 5208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00644962
X-RAY DIFFRACTIONf_angle_d0.83036745
X-RAY DIFFRACTIONf_chiral_restr0.0496764
X-RAY DIFFRACTIONf_plane_restr0.0061879
X-RAY DIFFRACTIONf_dihedral_angle_d14.86151870
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.606255812206
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.488138564593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-20.34331320.30032645X-RAY DIFFRACTION99.89
2-2.040.33491670.28282683X-RAY DIFFRACTION99.96
2.04-2.080.36611230.30912685X-RAY DIFFRACTION99.79
2.08-2.120.31111570.26692673X-RAY DIFFRACTION99.86
2.12-2.170.27681500.24792671X-RAY DIFFRACTION100
2.17-2.220.28331230.23892697X-RAY DIFFRACTION100
2.22-2.270.28421520.25882663X-RAY DIFFRACTION99.93
2.27-2.340.25831650.22762665X-RAY DIFFRACTION99.96
2.34-2.40.26811350.22252675X-RAY DIFFRACTION99.93
2.4-2.480.2781240.22372718X-RAY DIFFRACTION99.93
2.48-2.570.25461420.21852717X-RAY DIFFRACTION99.97
2.57-2.670.28381170.21842690X-RAY DIFFRACTION99.96
2.67-2.80.29021440.22992687X-RAY DIFFRACTION99.82
2.8-2.940.24221230.22342720X-RAY DIFFRACTION99.96
2.94-3.130.25191390.22912697X-RAY DIFFRACTION99.82
3.13-3.370.24731170.21152722X-RAY DIFFRACTION100
3.37-3.710.2331550.19532707X-RAY DIFFRACTION99.9
3.71-4.240.20651420.17962723X-RAY DIFFRACTION99.97
4.24-5.340.21981390.18352748X-RAY DIFFRACTION99.93
5.35-45.430.20361420.2272807X-RAY DIFFRACTION99.19

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