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- PDB-2zzo: Crystal structure of the complex between GP41 fragment N36 and fu... -

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Basic information

Entry
Database: PDB / ID: 2zzo
TitleCrystal structure of the complex between GP41 fragment N36 and fusion inhibitor C34/S138A
Components(Transmembrane protein) x 2
KeywordsVIRAL PROTEIN/INHIBITOR / HIV-1 / GP41 / VIRAL PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWatabe, T. / Nakano, H. / Nakatsu, T. / Kato, H. / Fujii, N.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: X-ray crystallographic study of an HIV-1 fusion inhibitor with the gp41 S138A substitution
Authors: Watabe, T. / Terakawa, Y. / Watanabe, K. / Ohno, H. / Nakano, H. / Nakatsu, T. / Kato, H. / Izumi, K. / Kodama, E. / Matsuoka, M. / Kitaura, K. / Oishi, S. / Fujii, N.
History
DepositionFeb 20, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
N: Transmembrane protein
C: Transmembrane protein


Theoretical massNumber of molelcules
Total (without water)8,4142
Polymers8,4142
Non-polymers00
Water48627
1
N: Transmembrane protein
C: Transmembrane protein

N: Transmembrane protein
C: Transmembrane protein

N: Transmembrane protein
C: Transmembrane protein


Theoretical massNumber of molelcules
Total (without water)25,2436
Polymers25,2436
Non-polymers00
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
Buried area11950 Å2
ΔGint-101 kcal/mol
Surface area11080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.090, 49.090, 56.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11N-3-

HOH

21N-7-

HOH

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Components

#1: Protein/peptide Transmembrane protein / TM / Glycoprotein 41 / gp41


Mass: 4152.843 Da / Num. of mol.: 1 / Fragment: GP41 FRAGMENT N36, UNP residues 546-581 / Source method: obtained synthetically / Details: PEPTIDE SYNTHESIS / References: UniProt: P04578, UniProt: P03377*PLUS
#2: Protein/peptide Transmembrane protein / TM / Glycoprotein 41 / gp41


Mass: 4261.615 Da / Num. of mol.: 1
Fragment: FUSION INHIBITOR PEPTIDE C34, UNP residues 628-661
Mutation: S138A / Source method: obtained synthetically / Details: PEPTIDE SYNTHESIS / References: UniProt: P04578, UniProt: P03377*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 293 K / pH: 4
Details: 100MM SODIUM ACETATE BUFFER, PH4.0, 400MM MAGNESIUM CHLORIDE, 12% ETHANOL, pH 4.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Oct 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→33.95 Å / Num. obs: 4248 / % possible obs: 99.7 % / Redundancy: 10.13 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 19.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 9.63 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 4.3 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AIK

1aik


Resolution: 2.2→18.52 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.675 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 195 4.6 %RANDOM
Rwork0.212 ---
obs0.215 4037 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.69 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→18.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms593 0 0 27 620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.021600
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.061.933810
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.326568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.8626.66736
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.22515116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.046153
X-RAY DIFFRACTIONr_chiral_restr0.1280.290
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02445
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2340.2240
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2434
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.217
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2950.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3791.5363
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2432563
X-RAY DIFFRACTIONr_scbond_it3.7513273
X-RAY DIFFRACTIONr_scangle_it6.0624.5247
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 12 -
Rwork0.185 292 -
obs--100 %

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