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- PDB-2b1h: Crystal structure analysis of anti-HIV-1 V3 Fab 2219 in complex w... -

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Basic information

Entry
Database: PDB / ID: 2b1h
TitleCrystal structure analysis of anti-HIV-1 V3 Fab 2219 in complex with UG29 peptide
Components
  • Fab 2219, heavy chain
  • Fab 2219, light chain
  • UG29 peptide of Exterior membrane glycoprotein GP120
KeywordsIMMUNE SYSTEM / Fab-peptide complex / HIV-1 / gp120 / v3 loop
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: UG29 peptide of Exterior membrane glycoprotein GP120


Theoretical massNumber of molelcules
Total (without water)49,7013
Polymers49,7013
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-26 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.899, 94.501, 96.617
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 UG29 peptide of Exterior membrane glycoprotein GP120 / gp120


Mass: 2596.017 Da / Num. of mol.: 1 / Fragment: residues 96-118 / Source method: obtained synthetically
Details: This sequence occurs in Human immunodeficiency virus type 1 (isolate MN)
References: GenBank: 50982993
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 25% MPEG 5000, 0.2M disodium tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 7, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→67.42 Å / Num. all: 39609 / Num. obs: 39609 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 33.6 Å2 / Rsym value: 0.069 / Net I/σ(I): 19.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 1963 / Rsym value: 0.612 / % possible all: 100

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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→67.42 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 9.471 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23837 1982 5 %RANDOM
Rwork0.20473 ---
all0.20646 37576 --
obs0.20646 37576 99.78 %-
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: 35.055 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20 Å2
2--2.5 Å20 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 2→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3449 0 0 123 3572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223543
X-RAY DIFFRACTIONr_bond_other_d0.0040.022380
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.9524827
X-RAY DIFFRACTIONr_angle_other_deg0.9673.0035822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3485453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91724.286133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33615548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2311512
X-RAY DIFFRACTIONr_chiral_restr0.1170.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023949
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02688
X-RAY DIFFRACTIONr_nbd_refined0.2180.2502
X-RAY DIFFRACTIONr_nbd_other0.1980.22354
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21678
X-RAY DIFFRACTIONr_nbtor_other0.0880.21824
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2151
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2330.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2151.52875
X-RAY DIFFRACTIONr_mcbond_other0.271.5918
X-RAY DIFFRACTIONr_mcangle_it1.49523670
X-RAY DIFFRACTIONr_scbond_it2.3831537
X-RAY DIFFRACTIONr_scangle_it3.2354.51157
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 134 -
Rwork0.327 2775 -
obs-2775 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)
11.8390.89940.21823.13060.69016.9399-0.12230.67680.6461-0.30150.33610.1283-0.7011-0.1956-0.2138-0.0704-0.0359-0.0188-0.0520.1572-0.007157.389646.372778.5174
26.74554.6591-1.35876.2328-1.64044.5921-0.11740.56750.6975-0.3470.28370.94290.0852-0.3176-0.16620.00490.0078-0.1387-0.13940.07120.052634.090728.182161.1943
33.43811.59420.35592.51160.25641.6626-0.0658-0.0180.36380.04970.03120.067-0.2094-0.03250.0347-0.24110.03410.0102-0.207-0.0055-0.18355.801933.5394.0439
45.97611.3945-0.65792.7831.075314.9028-0.35541.1684-0.4696-0.82840.17390.14681.2865-0.41260.18150.3188-0.0672-0.047-0.0676-0.1427-0.048737.753412.289360.2558
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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