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- PDB-2xt1: Crystal structure of the HIV-1 capsid protein C-terminal domain (... -

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Basic information

Entry
Database: PDB / ID: 2xt1
TitleCrystal structure of the HIV-1 capsid protein C-terminal domain (146- 231) in complex with a camelid VHH.
Components
  • CAMELID VHH 9
  • GAG POLYPROTEIN
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


viral process / viral capsid
Similarity search - Function
Retrovirus capsid C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / : / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / Immunoglobulins / Immunoglobulin-like ...Retrovirus capsid C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / : / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
VICUGNA PACOS (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsIgonet, S. / Vaney, M.C. / Bartonova, V. / Helma, J. / Rothbauer, U. / Leonhardt, H. / Stura, E. / Krausslich, H.-G. / Rey, F.A.
CitationJournal: To be Published
Title: Targeting HIV-1 Virion Formation with Nanobodies -Implications for the Design of Assembly Inhibitors
Authors: Igonet, S. / Vaney, M.C. / Bartonova, V. / Helma, J. / Rothbauer, U. / Leonhardt, H. / Stura, E. / Krausslich, H.-G. / Rey, F.A.
History
DepositionOct 3, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Derived calculations / Category: struct_conn / struct_conn_type
Revision 1.2Aug 14, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 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: GAG POLYPROTEIN
B: CAMELID VHH 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9294
Polymers22,7452
Non-polymers1842
Water4,882271
1
A: GAG POLYPROTEIN
B: CAMELID VHH 9
hetero molecules

A: GAG POLYPROTEIN
B: CAMELID VHH 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8588
Polymers45,4894
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area6610 Å2
ΔGint-33.9 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.060, 88.170, 35.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2017-

HOH

21B-2087-

HOH

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Components

#1: Protein GAG POLYPROTEIN / HIV-1 CAPSID PROTEIN


Mass: 9530.921 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 146-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Strain: NL4-3 / Plasmid: PET11C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIL / References: UniProt: Q71B32
#2: Antibody CAMELID VHH 9


Mass: 13213.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VICUGNA PACOS (alpaca) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE VHH RESIDUES (CHAIN B) ARE NUMBERED ACCORDING TO THE KABAT NUMBERING.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.3 % / Description: NONE
Crystal growDetails: 28-32 % W/V PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.32→44.1 Å / Num. obs: 45032 / % possible obs: 98.2 % / Observed criterion σ(I): 2.1 / Redundancy: 13.7 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.7
Reflection shellResolution: 1.32→1.39 Å / Redundancy: 5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / % possible all: 88.6

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Processing

Software
NameVersionClassification
BUSTER2.9.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2BUO, 1KXV

2buo

1kxv


Resolution: 1.32→35.54 Å / Cor.coef. Fo:Fc: 0.9647 / Cor.coef. Fo:Fc free: 0.9558 / SU R Cruickshank DPI: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.052 / SU Rfree Blow DPI: 0.053 / SU Rfree Cruickshank DPI: 0.05
Details: THE 6XHISTIDINE TAG AT THE C-TERMINAL END OF CHAIN B IS DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1835 2258 5.1 %RANDOM
Rwork0.1607 ---
obs0.1618 44606 98.42 %-
Displacement parametersBiso mean: 15.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.7394 Å20 Å20 Å2
2---1.0369 Å20 Å2
3---0.2975 Å2
Refine analyzeLuzzati coordinate error obs: 0.129 Å
Refinement stepCycle: LAST / Resolution: 1.32→35.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1521 0 12 271 1804
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011626HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.112206HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d582SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes42HARMONIC2
X-RAY DIFFRACTIONt_gen_planes243HARMONIC5
X-RAY DIFFRACTIONt_it1626HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.05
X-RAY DIFFRACTIONt_other_torsion14.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion209SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2132SEMIHARMONIC4
LS refinement shellResolution: 1.32→1.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2098 128 4.76 %
Rwork0.2241 2561 -
all0.2234 2689 -
obs--98.42 %

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