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- PDB-1tjg: Crystal Structure of the broadly neutralizing anti-HIV-1 antibody... -

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Basic information

Entry
Database: PDB / ID: 1tjg
TitleCrystal Structure of the broadly neutralizing anti-HIV-1 antibody 2F5 in complex with a gp41 7mer epitope
Components
  • Envelope glycoprotein GP41
  • FAB 2F5 Heavy Chain
  • FAB 2F5 Light Chain
KeywordsViral protein/Immune system / 2F5 / ANTIBODY / GP41 / HIV-1 / NEUTRALIZING / MEMBRANE-PROXIMAL / Viral protein-Immune system COMPLEX
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 ...symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / identical protein binding / 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
ISOPROPYL ALCOHOL / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOfek, G. / Tang, M. / Sambor, A. / Katinger, H. / Mascola, J.R. / Wyatt, R. / Kwong, P.D.
CitationJournal: J.Virol. / Year: 2004
Title: Structure and mechanistic analysis of the Anti-Human Immunodeficiency Virus Type 1 antibody 2F5 in complex with its gp41 epitope
Authors: Ofek, G. / Tang, M. / Sambor, A. / Katinger, H. / Mascola, J.R. / Wyatt, R. / Kwong, P.D.
History
DepositionJun 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THERE ARE CURRENTLY NO SEQUENCE DATABASE MATCHES FOR CHAINS L AND H. CHAINS L AND H ARE ...SEQUENCE THERE ARE CURRENTLY NO SEQUENCE DATABASE MATCHES FOR CHAINS L AND H. CHAINS L AND H ARE NUMBERED IN KABAT FORMAT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: FAB 2F5 Light Chain
H: FAB 2F5 Heavy Chain
P: Envelope glycoprotein GP41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,10513
Polymers49,4993
Non-polymers60710
Water7,044391
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.860, 64.020, 179.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide Envelope glycoprotein GP41


Mass: 848.920 Da / Num. of mol.: 1 / Fragment: Transmembrane Glycoprotein (residues 659-669) / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in the human immunodeficiency virus (HIV-1; strain JRFL).
References: UniProt: Q75760

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Antibody , 2 types, 2 molecules LH

#1: Antibody FAB 2F5 Light Chain


Mass: 23362.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Heteromyeloma cell line CB-F7 fused with peripheral blood mononuclear cells
Cell line (production host): CB-F7 / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody FAB 2F5 Heavy Chain


Mass: 25286.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Heteromyeloma cell line CB-F7 fused with peripheral blood mononuclear cells
Cell line (production host): CB-F7 / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 3 types, 401 molecules

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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 3.373 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 293 K / pH: 5.6
Details: 20% PEG 4000, 20% Isopropanol, 0.1M Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 12, 2003
RadiationMonochromator: SI (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 43466 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 14 Å2 / Rsym value: 0.089 / Net I/σ(I): 7.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.47 / Rsym value: 0.53 / % possible all: 92.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RZG

1rzg


Resolution: 2→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 440552.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.225 4108 10 %RANDOM
Rwork0.198 ---
obs0.198 40962 90.7 %-
all-45963 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.11 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å20 Å2
2--2.79 Å20 Å2
3----4.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3481 0 12 419 3912
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.252
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.262.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.311 486 9.7 %
Rwork0.279 4522 -
obs--66.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3IOH_XPLOR_PARAMIOH_XPLOR_TOP
X-RAY DIFFRACTION4EGL_XPLOR_PARAMEGL_XPLOR_TOP

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