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- PDB-4kht: Triple helix bundle of GP41 complexed with fab 8066 -

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Basic information

Entry
Database: PDB / ID: 4kht
TitleTriple helix bundle of GP41 complexed with fab 8066
Components
  • 8066 heavy chain
  • 8066 light chain
  • Gp41 helix
KeywordsIMMUNE SYSTEM / GP41 fab immune system
Function / homology
Function and homology information


viral envelope / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function
Retroviral envelope protein / Retroviral envelope protein GP41-like / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman Immunodeficiency Virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.817 Å
AuthorsLi, M. / Gustchina, A. / Wlodawer, A.
CitationJournal: Plos One / Year: 2013
Title: Complexes of neutralizing and non-neutralizing affinity matured Fabs with a mimetic of the internal trimeric coiled-coil of HIV-1 gp41.
Authors: Gustchina, E. / Li, M. / Ghirlando, R. / Schuck, P. / Louis, J.M. / Pierson, J. / Rao, P. / Subramaniam, S. / Gustchina, A. / Clore, G.M. / Wlodawer, A.
History
DepositionMay 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Structure summary / Category: audit_author / software / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gp41 helix
H: 8066 heavy chain
L: 8066 light chain


Theoretical massNumber of molelcules
Total (without water)56,5213
Polymers56,5213
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-36 kcal/mol
Surface area24380 Å2
MethodPISA
2
A: Gp41 helix
H: 8066 heavy chain
L: 8066 light chain

A: Gp41 helix
H: 8066 heavy chain
L: 8066 light chain

A: Gp41 helix
H: 8066 heavy chain
L: 8066 light chain


Theoretical massNumber of molelcules
Total (without water)169,5639
Polymers169,5639
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area22010 Å2
ΔGint-188 kcal/mol
Surface area65160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.416, 104.416, 97.127
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Gp41 helix


Mass: 7574.946 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human Immunodeficiency Virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: A1YNW7*PLUS
#2: Antibody 8066 heavy chain


Mass: 26305.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Antibody 8066 light chain


Mass: 22640.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10% PEG4k, 20%isopropranol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 12, 2012
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 14235 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rsym value: 0.063 / Net I/σ(I): 23.45
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.08 / Num. unique all: 929 / Rsym value: 0.328 / % possible all: 62.7

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.817→35.558 Å / SU ML: 0.43 / σ(F): 1.35 / Phase error: 31.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2656 716 5.04 %random
Rwork0.2146 ---
obs0.2171 14212 93.56 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 90.71 Å2 / ksol: 0.298 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--17.9822 Å20 Å20 Å2
2---17.9822 Å2-0 Å2
3---35.6595 Å2
Refinement stepCycle: LAST / Resolution: 2.817→35.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3688 0 0 0 3688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013774
X-RAY DIFFRACTIONf_angle_d1.3375133
X-RAY DIFFRACTIONf_dihedral_angle_d18.1691352
X-RAY DIFFRACTIONf_chiral_restr0.081583
X-RAY DIFFRACTIONf_plane_restr0.007659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.817-3.03440.4257980.32131989X-RAY DIFFRACTION70
3.0344-3.33950.31731640.26272753X-RAY DIFFRACTION98
3.3395-3.82230.27981690.21542835X-RAY DIFFRACTION100
3.8223-4.81370.20891370.18572907X-RAY DIFFRACTION100
4.8137-35.56110.26811480.21163012X-RAY DIFFRACTION100
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)
11.5608-0.26390.21440.14490.39251.89450.57171.5037-0.03760.257-1.37460.13790.04440.2753-0.27692.48640.71020.01072.9705-0.48760.633155.338924.3882-41.0647
21.6855-0.465-1.34381.08010.06336.0823-0.85320.4162-0.022-0.643-0.43150.9431-0.34-0.5399-0.01770.8705-0.1226-0.04821.00410.10450.046646.946229.23447.2308
37.18770.877-0.32285.3541-0.8273.09790.141-0.5868-0.49960.1398-0.05270.7167-0.10280.2389-0.07410.3934-0.00270.08190.4609-0.03440.350329.683826.502728.1294
43.20080.66830.96932.14630.02292.43490.35580.8285-0.3128-0.4110.58251.91820.6859-0.6841-0.51421.0451-0.1823-0.18841.36180.0291.95331.680917.114324.8663
53.8267-2.3588-1.11783.501-1.36622.910.02290.76081.8258-0.40270.27041.4966-0.738-0.4137-0.230.74790.1001-0.03720.7370.2451.454523.696944.57817.8718
60.9013-0.6568-0.27330.7752-0.20830.877-0.47860.28010.12540.21340.24891.54730.3918-1.5668-0.2181-0.1776-0.110.15941.66840.82693.1486-10.349328.775728.6333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:26 )A2 - 26
2X-RAY DIFFRACTION2( CHAIN A AND RESID 27:67 )A27 - 67
3X-RAY DIFFRACTION3( CHAIN H AND RESID 3:119 )H3 - 119
4X-RAY DIFFRACTION4( CHAIN H AND RESID 143:220 )H143 - 220
5X-RAY DIFFRACTION5( CHAIN L AND RESID 2:109 )L2 - 109
6X-RAY DIFFRACTION6( CHAIN L AND RESID 110:210 )L110 - 210

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