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- PDB-2b1a: Crystal structure analysis of anti-HIV-1 V3 Fab 2219 in complex w... -

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Basic information

Entry
Database: PDB / ID: 2b1a
TitleCrystal structure analysis of anti-HIV-1 V3 Fab 2219 in complex with UG1033 peptide
Components
  • Fab 2219, heavy chain
  • Fab 2219, light chain
  • UG1033 peptide of Exterior membrane glycoprotein GP120
KeywordsIMMUNE SYSTEM / Fab-peptide complex / HIV-1 / gp120 / v3 loop
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / : / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane ...virus-mediated perturbation of host defense response => GO:0019049 / : / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.348 Å
AuthorsStanfield, R.L. / Gorny, M.K. / Zolla-Pazner, S. / Wilson, I.A.
CitationJournal: J.Virol. / Year: 2006
Title: Crystal structures of human immunodeficiency virus type 1 (HIV-1) neutralizing antibody 2219 in complex with three different V3 peptides reveal a new binding mode for HIV-1 cross-reactivity.
Authors: Stanfield, R.L. / Gorny, M.K. / Zolla-Pazner, S. / Wilson, I.A.
History
DepositionSep 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab 2219, light chain
H: Fab 2219, heavy chain
P: UG1033 peptide of Exterior membrane glycoprotein GP120


Theoretical massNumber of molelcules
Total (without water)49,5683
Polymers49,5683
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-27 kcal/mol
Surface area20510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.716, 96.890, 97.018
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: Antibody Fab 2219, light chain


Mass: 22949.303 Da / Num. of mol.: 1 / Fragment: light chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: peripheral blood cells / Organ: blood
#2: Antibody Fab 2219, heavy chain


Mass: 24155.715 Da / Num. of mol.: 1 / Fragment: heavy chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: peripheral blood cells / Organ: blood
#3: Protein/peptide UG1033 peptide of Exterior membrane glycoprotein GP120 / gp120


Mass: 2462.764 Da / Num. of mol.: 1 / Fragment: residues 31-53 / Source method: obtained synthetically
Details: This sequence occurs in Human immunodeficiency virus type 1 (isolate MN)
References: GenBank: 313516, UniProt: Q90VI2*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.95 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 13.75% PEG 20000, 0.05M disodium tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98397 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 9, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98397 Å / Relative weight: 1
ReflectionResolution: 2.348→31.31 Å / Num. all: 24986 / Num. obs: 24986 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 56 Å2 / Rsym value: 0.057 / Net I/σ(I): 31.9
Reflection shellResolution: 2.348→2.39 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.36 / Num. unique all: 1118 / Rsym value: 0.488 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.2refinement
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B0S

2b0s


Resolution: 2.348→31.31 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 17.155 / SU ML: 0.199 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.302 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24446 1208 4.8 %RANDOM
Rwork0.21118 ---
all0.21287 23732 --
obs0.21287 23732 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 59.833 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2--0.6 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.348→31.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3440 0 0 60 3500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223535
X-RAY DIFFRACTIONr_bond_other_d0.0010.022366
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.9514818
X-RAY DIFFRACTIONr_angle_other_deg0.8493.0035785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7265453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41624.211133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.90415539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2361512
X-RAY DIFFRACTIONr_chiral_restr0.0790.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023951
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02690
X-RAY DIFFRACTIONr_nbd_refined0.1990.2528
X-RAY DIFFRACTIONr_nbd_other0.1970.22311
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21632
X-RAY DIFFRACTIONr_nbtor_other0.0850.21931
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2128
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.110.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0740.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6281.52893
X-RAY DIFFRACTIONr_mcbond_other0.0991.5920
X-RAY DIFFRACTIONr_mcangle_it0.73923663
X-RAY DIFFRACTIONr_scbond_it1.22231529
X-RAY DIFFRACTIONr_scangle_it1.834.51155
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.348→2.409 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 83 -
Rwork0.364 1598 -
obs-1598 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.13181.72670.60793.58990.05979.3013-0.10560.65910.8465-0.30490.46420.397-0.9478-0.3733-0.3586-0.16810.06960.0674-0.09990.2511-0.010957.554647.698379.9572
27.62562.9285-0.38258.2275-3.22216.7096-0.00930.10940.5159-1.17830.41921.40370.55-0.6781-0.40990.1159-0.0032-0.3476-0.16730.06310.043134.363530.490161.6951
34.19232.46670.47893.39130.35811.86690.0976-0.00060.35450.0982-0.02820.1113-0.2599-0.1268-0.0694-0.41670.04930.0516-0.26610.0056-0.306555.733833.769494.7209
44.38262.2038-0.67878.7053-1.814114.2058-0.49170.6005-0.3217-3.22640.29310.55362.2095-0.22420.19861.0551-0.0474-0.186-0.2147-0.1162-0.172438.255314.809660.0755
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LA1 - 1071 - 113
2X-RAY DIFFRACTION2LA108 - 212114 - 215
3X-RAY DIFFRACTION3HB1 - 1131 - 124
4X-RAY DIFFRACTION3PC303 - 3203 - 18
5X-RAY DIFFRACTION4HB114 - 229125 - 226

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