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- PDB-3fn0: Crystal structure of HIV-1 neutralizing human Fab Z13e1 in comple... -

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Basic information

Entry
Database: PDB / ID: 3fn0
TitleCrystal structure of HIV-1 neutralizing human Fab Z13e1 in complex with a 12-residue peptide containing the Z13e1 epitope on gp41
Components
  • (Fab Z13e1) x 2
  • Envelope polyprotein gp160
KeywordsIMMUNE SYSTEM / Z13e1 / Z13 / HIV / ENV / GP41
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPejchal, R. / Wilson, I.A. / Zwick, M.B.
CitationJournal: J.Virol. / Year: 2009
Title: A conformational switch in human immunodeficiency virus gp41 revealed by the structures of overlapping epitopes recognized by neutralizing antibodies.
Authors: Pejchal, R. / Gach, J.S. / Brunel, F.M. / Cardoso, R.M. / Stanfield, R.L. / Dawson, P.E. / Burton, D.R. / Zwick, M.B. / Wilson, I.A.
History
DepositionDec 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab Z13e1
H: Fab Z13e1
P: Envelope polyprotein gp160


Theoretical massNumber of molelcules
Total (without water)49,0753
Polymers49,0753
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-29 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.940, 106.940, 88.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11L-340-

HOH

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Components

#1: Antibody Fab Z13e1


Mass: 23096.691 Da / Num. of mol.: 1 / 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 Z13e1


Mass: 24753.883 Da / Num. of mol.: 1 / 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 Envelope polyprotein gp160


Mass: 1224.343 Da / Num. of mol.: 1 / Fragment: transmembrane glycoprotein / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 21% PEG 3350, 0.2M potassium fluoride, 0.1M sodium chloride, 10mM Tris-Cl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.99996 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 17, 2008
RadiationMonochromator: single crystal Si(111) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 1.8→29.7 Å / Num. all: 48242 / Num. obs: 48156 / % possible obs: 99.8 % / Redundancy: 14.3 % / Biso Wilson estimate: 29.2 Å2 / Rsym value: 0.047 / Net I/σ(I): 33.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 14.6 % / Mean I/σ(I) obs: 6.1 / Num. unique all: 3528 / Rsym value: 0.481 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
EPMRphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NXY

2nxy


Resolution: 1.8→29.66 Å / SU ML: 0.04 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 2408 5 %RANDOM
Rwork0.2098 ---
obs0.212 48152 99.85 %-
all-48242 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.447 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 40.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.8897 Å20 Å20 Å2
2---1.8897 Å20 Å2
3---3.7795 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3293 0 0 230 3523
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.016
X-RAY DIFFRACTIONf_angle_deg1.553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83680.33711390.28782654X-RAY DIFFRACTION100
1.8368-1.87670.29241400.26962644X-RAY DIFFRACTION100
1.8767-1.92030.33961390.26072658X-RAY DIFFRACTION100
1.9203-1.96840.29851400.27042643X-RAY DIFFRACTION100
1.9684-2.02160.32891400.25832672X-RAY DIFFRACTION100
2.0216-2.0810.28681400.24412650X-RAY DIFFRACTION100
2.081-2.14820.28821390.24552649X-RAY DIFFRACTION100
2.1482-2.22490.29021420.22682690X-RAY DIFFRACTION100
2.2249-2.3140.231400.21742665X-RAY DIFFRACTION100
2.314-2.41930.24361400.20972669X-RAY DIFFRACTION100
2.4193-2.54670.2741430.2092705X-RAY DIFFRACTION100
2.5467-2.70620.27041400.21772671X-RAY DIFFRACTION100
2.7062-2.9150.2631430.22132709X-RAY DIFFRACTION100
2.915-3.2080.26121420.21842694X-RAY DIFFRACTION100
3.208-3.67150.25691440.2022749X-RAY DIFFRACTION100
3.6715-4.62290.19941460.15962768X-RAY DIFFRACTION100
4.6229-29.66380.19241510.15582854X-RAY DIFFRACTION98
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)
14.43260.7271-2.38211.00420.72042.2195-0.57350.2662-0.78830.10320.3154-0.29350.5064-0.05240.24540.2697-0.06850.07760.1609-0.0840.319440.054222.826249.178
21.03950.647-1.07630.5820.51062.4421-0.03460.20220.3534-0.00080.17760.2657-0.0793-0.2448-0.17190.1955-0.0001-0.0210.15280.06750.286518.652143.93468.0509
34.48390.5298-3.48030.63860.11543.2860.0257-0.9255-0.03970.02270.1251-0.22540.03440.9064-0.15020.083-0.0049-0.02720.432-0.14110.25856.078337.622553.1092
42.5201-0.4511-0.84873.09731.56363.1516-0.1598-0.67840.26820.25660.5536-0.12770.22410.4809-0.28880.18220.0687-0.03370.3135-0.0820.15631.064642.112578.411
5-4.84091.844-6.10330.62111.37777.852-0.2637-0.4132-0.3872-0.44390.2483-0.14030.18390.7583-0.13780.16560.04560.01330.4014-0.15010.417465.037131.275139.9106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain L and resid 3:108
2X-RAY DIFFRACTION2chain L and resid 109:211
3X-RAY DIFFRACTION3chain H and resid 1:113
4X-RAY DIFFRACTION4chain H and resid 114:227
5X-RAY DIFFRACTION5chain P and resid 670:678

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