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- PDB-4khx: Crystal structure of gp41 helix complexed with antibody 8062 -

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Basic information

Entry
Database: PDB / ID: 4khx
TitleCrystal structure of gp41 helix complexed with antibody 8062
Components
  • 8062 heavy chain
  • 8062 light chain
  • gp41 helix
KeywordsIMMUNE SYSTEM / gp41
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: 2.921 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 / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: gp41 helix
H: 8062 heavy chain
L: 8062 light chain


Theoretical massNumber of molelcules
Total (without water)56,5503
Polymers56,5503
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-33 kcal/mol
Surface area24630 Å2
MethodPISA
2
A: gp41 helix
H: 8062 heavy chain
L: 8062 light chain

A: gp41 helix
H: 8062 heavy chain
L: 8062 light chain

A: gp41 helix
H: 8062 heavy chain
L: 8062 light chain


Theoretical massNumber of molelcules
Total (without water)169,6509
Polymers169,6509
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 area23750 Å2
ΔGint-181 kcal/mol
Surface area64570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.814, 106.814, 98.537
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 8062 heavy chain


Mass: 26334.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Antibody 8062 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: 2.87 Å3/Da / Density % sol: 57.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10% PEG4000, 20% isopropanol, 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: 2.921→50 Å / Num. all: 13242 / Num. obs: 13242 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rsym value: 0.094 / Net I/σ(I): 20.47
Reflection shellResolution: 3→3.05 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 427 / Rsym value: 0.41 / % possible all: 63.7

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.921→30.952 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 35.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2895 663 5.01 %random
Rwork0.2366 ---
obs0.2393 13236 91.43 %-
all-13242 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.397 Å2 / ksol: 0.278 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--14.3197 Å2-0 Å20 Å2
2---14.3197 Å2-0 Å2
3---40.0112 Å2
Refinement stepCycle: LAST / Resolution: 2.921→30.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3625 0 0 0 3625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043709
X-RAY DIFFRACTIONf_angle_d0.8045039
X-RAY DIFFRACTIONf_dihedral_angle_d16.7911323
X-RAY DIFFRACTIONf_chiral_restr0.055574
X-RAY DIFFRACTIONf_plane_restr0.005643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9212-3.14660.4196940.3361785X-RAY DIFFRACTION66
3.1466-3.46290.38261560.30152668X-RAY DIFFRACTION99
3.4629-3.96310.3851370.30452524X-RAY DIFFRACTION93
3.9631-4.98970.26741280.20832769X-RAY DIFFRACTION100
4.9897-30.95410.23681480.20592827X-RAY DIFFRACTION99
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)
11.7982-0.72350.89472.00480.84891.4267-0.16250.6763-0.288-0.3066-0.2884-0.07950.5736-0.79860.01890.86390.015-0.11510.8556-0.15930.596254.653325.8618-30.3567
22.6790.0934-1.58482.0504-1.44311.7808-0.3324-0.2746-0.18860.133-0.2340.796-0.3601-0.63830.00310.57260.0237-0.03330.63280.04940.597147.311431.576717.8144
37.13420.09-0.82154.8351-1.07482.4040.0284-0.6002-0.54980.03710.16410.1764-0.17190.0568-0.00040.68320.03110.09820.65570.00990.650830.659126.739629.3557
43.44490.17420.17833.3324-1.44810.81650.65040.3413-0.8007-0.76910.70532.24080.55950.32950.03011.2571-0.1211-0.34021.0989-0.06141.94061.888618.840126.5976
53.5084-3.92421.48015.3981-2.33925.1363-0.15840.08780.3967-0.33910.055-0.1417-0.77170.2380.07340.8114-0.04490.07750.7493-0.0630.880224.21745.306719.1368
61.57250.75751.12950.92510.87990.9068-0.30830.3206-0.7788-0.93350.55512.6454-0.1713-1.09930.04490.51570.00710.26271.56930.70283.2847-9.236730.767931.0604
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:39 )A2 - 39
2X-RAY DIFFRACTION2( CHAIN A AND RESID 40:67 )A40 - 67
3X-RAY DIFFRACTION3( CHAIN H AND RESID 3:119 )H3 - 119
4X-RAY DIFFRACTION4( CHAIN H AND RESID 120:218 )H120 - 218
5X-RAY DIFFRACTION5( CHAIN L AND RESID 2:114 )L2 - 114
6X-RAY DIFFRACTION6( CHAIN L AND RESID 115:208 )L115 - 208

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