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

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Basic information

Entry
Database: PDB / ID: 1tji
TitleCrystal Structure of the broadly neutralizing anti-HIV-1 antibody 2F5 in complex with a gp41 17mer epitope
Components
  • (anti-HIV-1 antibody 2F5 ...) x 2
  • Envelope Glycoprotein GP41
KeywordsViral protein/Immune system / 2F5 / antibody / gp41 / HIV-1 / neutralizing / membrane-proximal / Viral protein-Immune system COMPLEX
Function / homology
Function and homology information


Dectin-2 family / 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 ...Dectin-2 family / 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 / 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 / DIFFERENCE FOURIER METHOD / Resolution: 2.2 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_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

Downloads & links

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Assembly

Deposited unit
L: anti-HIV-1 antibody 2F5 Light Chain
H: anti-HIV-1 antibody 2F5 Heavy Chain
P: Envelope Glycoprotein GP41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,32812
Polymers50,7813
Non-polymers5479
Water9,962553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-11 kcal/mol
Surface area21450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.660, 63.684, 178.375
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: 2131.364 Da / Num. of mol.: 1 / Fragment: Transmembrane Glycoprotein (residues 653-659) / 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: P04580

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Antibody , 2 types, 2 molecules LH

#1: Antibody anti-HIV-1 antibody 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 fused with peripheral blood mononuclear cells
Cell line (production host): CB-F7 / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody anti-HIV-1 antibody 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 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, 562 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.: 6 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / 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: 3.296 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / pH: 5.6
Details: 20% PEG 4000, 20% Isopropanol, 0.125 M NaCitrate, 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: Oct 31, 2003
RadiationMonochromator: SI (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 32958 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 22.3 Å2 / Rsym value: 0.126 / Net I/σ(I): 14.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.95 / Rsym value: 0.494 / % possible all: 75.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER METHOD
Starting model: PDB ENTRY 1TJH

1tjh


Resolution: 2.2→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 332712.1 / 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
Rfree0.221 3104 10 %RANDOM
Rwork0.183 ---
obs0.183 30875 89.3 %-
all-46092 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.29 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.44 Å20 Å20 Å2
2---2.94 Å20 Å2
3----0.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3546 0 12 577 4135
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
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_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.322
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.182.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 380 10.7 %
Rwork0.261 3160 -
obs--62 %
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.TXT
X-RAY DIFFRACTION4EGL_XPLOR_PARAMEGL_XPLOR_TOP.TXT
X-RAY DIFFRACTION5CAPPING.PARAMCAPPING.TOP

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