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- PDB-1tsu: CRYSTAL STRUCTURE OF DECAMER NCP1 SUBSTRATE PEPTIDE IN COMPLEX WI... -

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Basic information

Entry
Database: PDB / ID: 1tsu
TitleCRYSTAL STRUCTURE OF DECAMER NCP1 SUBSTRATE PEPTIDE IN COMPLEX WITH WILD-TYPE D25N HIV-1 PROTEASE VARIANT
Components
  • NC-P1 SUBSTRATE PEPTIDE
  • Pol polyprotein
KeywordsViral protein/hydrolase / CO-EVOLUTION / NUCLEOCAPDIS / SUBSTRATE RECOGNITION / HIV-1 PROTEASE / Viral protein-hydrolase COMPLEX
Function / homology
Function and homology information


host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs ...host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / viral budding via host ESCRT complex / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / Membrane binding and targetting of GAG proteins / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal ...Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Gag-Pol polyprotein / Gag polyprotein
Similarity search - Component
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPrabu-Jeyabalan, M. / Nalivaika, E.A. / King, N.M. / Schiffer, C.A.
CitationJournal: J.Virol. / Year: 2004
Title: Structural basis for coevolution of a human immunodeficiency virus type 1 nucleocapsid-p1 cleavage site with a V82A drug-resistant mutation in viral protease
Authors: Prabu-Jeyabalan, M. / Nalivaika, E.A. / King, N.M. / Schiffer, C.A.
History
DepositionJun 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pol polyprotein
B: Pol polyprotein
P: NC-P1 SUBSTRATE PEPTIDE


Theoretical massNumber of molelcules
Total (without water)22,5373
Polymers22,5373
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-30 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.058, 57.731, 61.495
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pol polyprotein


Mass: 10800.777 Da / Num. of mol.: 2 / Fragment: Protease / Mutation: Q7K,D25N,L63P / Source method: obtained synthetically / References: UniProt: P03369, HIV-1 retropepsin
#2: Protein/peptide NC-P1 SUBSTRATE PEPTIDE


Mass: 935.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P04591
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.01 Å3/Da / Density % sol: 38.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: SODIUM PHOSPHATE, SODIUM CITRATE, AMMONIUM SULPHATE, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 220 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 29, 2002 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→42.26 Å / Num. all: 10450 / Num. obs: 10450 / % possible obs: 94.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.092

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MTR

1mtr


Resolution: 2.1→42.26 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.56 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.329 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23355 493 4.7 %RANDOM
Rwork0.20587 ---
obs0.20717 9912 93.93 %-
all-9912 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.067 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2---0.34 Å20 Å2
3---1.34 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1526 0 0 112 1638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221553
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9682116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2865203
X-RAY DIFFRACTIONr_chiral_restr0.1780.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021155
X-RAY DIFFRACTIONr_nbd_refined0.2480.2656
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.520.278
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4650.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.310.24
X-RAY DIFFRACTIONr_mcbond_it3.6231.51017
X-RAY DIFFRACTIONr_mcangle_it5.12821633
X-RAY DIFFRACTIONr_scbond_it7.2253536
X-RAY DIFFRACTIONr_scangle_it9.9614.5483
LS refinement shellResolution: 2.1→2.214 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.4 62
Rwork0.338 1244

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