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- PDB-2b0s: Crystal structure analysis of anti-HIV-1 V3 Fab 2219 in complex w... -

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Basic information

Entry
Database: PDB / ID: 2b0s
TitleCrystal structure analysis of anti-HIV-1 V3 Fab 2219 in complex with MN peptide
Components
  • Fab 2219, heavy chain
  • Fab 2219, light chain
  • MN peptide of Exterior membrane glycoprotein GP120
KeywordsIMMUNE SYSTEM / Fab-peptide complex / HIV-1 / gp120 / v3 loop
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / 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 / membrane / identical protein binding
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
ACETIC ACID / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 14, 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: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.name / _software.version
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: MN peptide of Exterior membrane glycoprotein GP120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6318
Polymers49,3273
Non-polymers3045
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-22 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.471, 60.471, 275.194
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide MN peptide of Exterior membrane glycoprotein GP120 / gp120


Mass: 2221.630 Da / Num. of mol.: 1 / Fragment: residues 308-325 / Source method: obtained synthetically
Details: This sequence occurs in Human immunodeficiency virus type 1 (isolate MN)
References: UniProt: P05877

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Antibody , 2 types, 2 molecules LH

#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

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Non-polymers , 3 types, 196 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 40% PEG 400, 0.2M potassium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.033 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.3→69.01 Å / Num. all: 23835 / Num. obs: 23835 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 30.8 Å2 / Rsym value: 0.086 / Net I/σ(I): 22
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 1162 / Rsym value: 0.525 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2refinement
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 7FAB

7fab


Resolution: 2.3→69.01 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.917 / SU B: 13.271 / SU ML: 0.17 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.344 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26665 1195 5 %RANDOM
Rwork0.21685 ---
all0.21926 22624 --
obs0.21926 22624 99.81 %-
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: 31.648 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20 Å2
2--0.95 Å20 Å2
3----1.89 Å2
Refinement stepCycle: LAST / Resolution: 2.3→69.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3449 0 20 191 3660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223558
X-RAY DIFFRACTIONr_bond_other_d0.0020.023066
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9544840
X-RAY DIFFRACTIONr_angle_other_deg0.9237199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2315453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71624.104134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88215545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0491513
X-RAY DIFFRACTIONr_chiral_restr0.130.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023968
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02694
X-RAY DIFFRACTIONr_nbd_refined0.2060.2550
X-RAY DIFFRACTIONr_nbd_other0.1890.23029
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21651
X-RAY DIFFRACTIONr_nbtor_other0.0850.22127
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2224
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.27
X-RAY DIFFRACTIONr_mcbond_it0.7511.52884
X-RAY DIFFRACTIONr_mcbond_other0.1271.5929
X-RAY DIFFRACTIONr_mcangle_it0.93723670
X-RAY DIFFRACTIONr_scbond_it1.49431553
X-RAY DIFFRACTIONr_scangle_it2.1334.51170
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 75 -
Rwork0.276 1643 -
obs-1643 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)
16.1882-0.76330.10150.7634-0.59571.74840.01820.57430.0324-0.3117-0.0874-0.26250.11480.02550.0692-0.00680.01350.0421-0.13470.0385-0.124624.584161.8127144.2352
21.908-0.4362-0.08355.9426-3.18324.78090.13410.2237-0.2653-0.1342-0.03330.03680.5044-0.3384-0.1009-0.0179-0.0304-0.009-0.0657-0.0019-0.042443.370337.9077151.6725
31.4146-0.49270.66421.8712-1.25912.79120.02710.0205-0.02270.06740.00070.0808-0.0228-0.1118-0.0279-0.0829-0.01040.016-0.2365-0.0095-0.149714.340259.2174161.8069
47.83890.0011-1.11812.3965-1.21012.4069-0.03010.1349-0.2679-0.0692-0.0086-0.21770.2718-0.02250.03870.0354-0.0034-0.0402-0.16070.0304-0.050452.827138.7713165.0012
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 - 3201 - 16
5X-RAY DIFFRACTION4HB114 - 229125 - 226

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