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- PDB-1tzg: Crystal structure of HIV-1 neutralizing human Fab 4E10 in complex... -

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Basic information

Entry
Database: PDB / ID: 1tzg
TitleCrystal structure of HIV-1 neutralizing human Fab 4E10 in complex with a 13-residue peptide containing the 4E10 epitope on gp41
Components
  • (Fab 4E10) x 2
  • Envelope polyprotein GP160
KeywordsIMMUNE SYSTEM / antibody-epitope complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCardoso, R.M.F. / Zwick, M.B. / Stanfield, R.L. / Kunert, R. / Binley, J.M. / Katinger, H. / Burton, D.R. / Wilson, I.A.
CitationJournal: 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
DepositionJul 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE A suitable database reference sequence could not be found for the protein chains in this ...SEQUENCE A suitable database reference sequence could not be found for the protein chains in this structure at the time of processing

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab 4E10
H: Fab 4E10
M: Fab 4E10
I: Fab 4E10
P: Envelope polyprotein GP160
Q: Envelope polyprotein GP160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0189
Polymers98,7426
Non-polymers2763
Water11,025612
1
L: Fab 4E10
H: Fab 4E10
P: Envelope polyprotein GP160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6476
Polymers49,3713
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-32 kcal/mol
Surface area21270 Å2
MethodPISA
2
M: Fab 4E10
I: Fab 4E10
Q: Envelope polyprotein GP160


Theoretical massNumber of molelcules
Total (without water)49,3713
Polymers49,3713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-33 kcal/mol
Surface area20880 Å2
MethodPISA
3
L: Fab 4E10
H: Fab 4E10
P: Envelope polyprotein GP160
hetero molecules

M: Fab 4E10
I: Fab 4E10
Q: Envelope polyprotein GP160


Theoretical massNumber of molelcules
Total (without water)99,0189
Polymers98,7426
Non-polymers2763
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_444x-1/2,y-1/2,z-11
Buried area11360 Å2
ΔGint-85 kcal/mol
Surface area40370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.300, 45.100, 198.500
Angle α, β, γ (deg.)90.00, 113.80, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe asymmetric unit contains two biological units (2 Fab-peptide complexes)

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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) / Cell (production host): ovary / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab 4E10


Mass: 24424.518 Da / Num. of mol.: 2 / Fragment: heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): ovary / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide Envelope polyprotein GP160 / GP41


Mass: 1653.837 Da / Num. of mol.: 2 / Fragment: Transmembrane glycoprotein / Source method: obtained synthetically
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 3.26 Å3/Da / Density % sol: 62.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG 8000, sodium acetate, hexamine cobalt trichloride, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979126 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2003
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979126 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 61572 / % possible obs: 93 % / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Biso Wilson estimate: 23.9 Å2 / Rsym value: 0.075 / Net I/σ(I): 16.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 4037 / Rsym value: 0.371 / % possible all: 61.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HKL

1hkl


Resolution: 2.2→43 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 3091 -random
Rwork0.217 ---
all-61322 --
obs-61322 93.2 %-
Solvent computationBsol: 42.178 Å2 / ksol: 0.329003 e/Å3
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.361 Å20 Å2-0.955 Å2
2---4.981 Å20 Å2
3---3.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6904 0 18 612 7534
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.3081.5
X-RAY DIFFRACTIONc_scbond_it2.0572
X-RAY DIFFRACTIONc_mcangle_it2.1122
X-RAY DIFFRACTIONc_scangle_it2.8992.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.286 394 -
Rwork0.265 --
obs-7638 70.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2glycerol.param
X-RAY DIFFRACTION3CNS_TOPPAR:water.param

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