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- PDB-2fx9: Crystal structure of hiv-1 neutralizing human fab 4e10 in complex... -

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Basic information

Entry
Database: PDB / ID: 2fx9
TitleCrystal structure of hiv-1 neutralizing human fab 4e10 in complex with a thioether-linked peptide encompassing the 4e10 epitope on gp41
Components
  • (Fab 4E10) x 2
  • Fragment of HIV glycoprotein gp41
KeywordsIMMUNE SYSTEM / immunoglobulin fold / beta-sandwich / antibody-epitope 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
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCardoso, R.M.F. / Brunel, F.M. / Ferguson, S. / Burton, D.R. / Dawson, P.E. / Wilson, I.A.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Structural basis of enhanced binding of extended and helically constrained peptide epitopes of the broadly neutralizing HIV-1 antibody 4E10.
Authors: Cardoso, R.M. / Brunel, F.M. / Ferguson, S. / Zwick, M. / Burton, D.R. / Dawson, P.E. / Wilson, I.A.
#1: Journal: Immunity / Year: 2005
Title: Broadly neutralizing anti-HIV antibody 4E10 recognizes a helical conformation of a highly conserved fusion-associated motif in gp41
Authors: Cardoso, R.M.F. / Zwick, M.B. / Stanfield, R.L. / Kunert, R. / Binley, J.M. / Katinger, H. / Burton, D.R. / Wilson, I.A.
History
DepositionFeb 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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
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_atom_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 999No database reference is currently available for Chains L, M, H, I, P, and Q.

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
L: Fab 4E10
H: Fab 4E10
M: Fab 4E10
I: Fab 4E10
P: Fragment of HIV glycoprotein gp41
Q: Fragment of HIV glycoprotein gp41


Theoretical massNumber of molelcules
Total (without water)98,1906
Polymers98,1906
Non-polymers00
Water7,260403
1
L: Fab 4E10
H: Fab 4E10
P: Fragment of HIV glycoprotein gp41


Theoretical massNumber of molelcules
Total (without water)49,0953
Polymers49,0953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-38 kcal/mol
Surface area20410 Å2
MethodPISA
2
M: Fab 4E10
I: Fab 4E10
Q: Fragment of HIV glycoprotein gp41


Theoretical massNumber of molelcules
Total (without water)49,0953
Polymers49,0953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-37 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.425, 111.498, 79.379
Angle α, β, γ (deg.)90.00, 106.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab 4E10


Mass: 23292.705 Da / Num. of mol.: 2 / Fragment: Light Chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab 4E10


Mass: 23860.848 Da / Num. of mol.: 2 / Fragment: Heavy Chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide Fragment of HIV glycoprotein gp41


Mass: 1941.385 Da / Num. of mol.: 2 / Fragment: Peptide Epitope of 4E10 / Source method: obtained synthetically
Details: This sequence includes a fragment of the HIV envelope protein gp41
References: UniProt: P05880*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.2 M ammonium nitrate, pH no buffer, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.95369 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 5, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 51978 / Num. obs: 51614 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 31.6 Å2 / Rsym value: 0.094 / Net I/σ(I): 14.1
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 3779 / Rsym value: 0.324 / % possible all: 99

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Processing

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

1tzg


Resolution: 2.1→50 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2560 -RANDOM
Rwork0.236 ---
all-51990 --
obs-51545 99.1 %-
Solvent computationBsol: 46.1188 Å2 / ksol: 0.343825 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1-9.568 Å20 Å20.928 Å2
2---8.225 Å20 Å2
3----1.343 Å2
Refine analyzeLuzzati coordinate error obs: 0.316 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6916 0 0 403 7319
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_mcbond_it1.433
X-RAY DIFFRACTIONc_scangle_it2.952
X-RAY DIFFRACTIONc_scbond_it2.043
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.1-2.110.334550.304X-RAY DIFFRACTION943
2.11-2.130.334470.304X-RAY DIFFRACTION1012

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