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- PDB-3p30: crystal structure of the cluster II Fab 1281 in complex with HIV-... -

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Basic information

Entry
Database: PDB / ID: 3p30
Titlecrystal structure of the cluster II Fab 1281 in complex with HIV-1 gp41 ectodomain
Components
  • 1281 Fab heavy chain
  • 1281 Fab light chain
  • HIV-1 gp41
KeywordsIMMUNE SYSTEM / HIV / gp41 / cluster 2 / Fab / 6-helix bundle
Function / homologyHelix Hairpins - #210 / Helix Hairpins / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Function and homology information
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsFrey, G. / Chen, J. / Rits-Volloch, S. / Freeman, M.M. / Zolla-Pazner, S. / Chen, B.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Distinct conformational states of HIV-1 gp41 are recognized by neutralizing and non-neutralizing antibodies.
Authors: Frey, G. / Chen, J. / Rits-Volloch, S. / Freeman, M.M. / Zolla-Pazner, S. / Chen, B.
History
DepositionOct 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 gp41
L: 1281 Fab light chain
H: 1281 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)57,7783
Polymers57,7783
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-68 kcal/mol
Surface area13300 Å2
Unit cell
Length a, b, c (Å)115.830, 115.830, 119.544
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein HIV-1 gp41


Mass: 11177.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 ENV / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Antibody 1281 Fab light chain


Mass: 22616.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HYBRIDOMA CELL / Production host: homo sapiens (human)
#3: Antibody 1281 Fab heavy chain


Mass: 23983.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HYBRIDOMA CELL / Production host: homo sapiens (human)
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THE GEN BANK ACCESSION CODE FOR 'HIV-1 ENV' 92UG037.8 (HIV1, SAMPLE 037 CLONE 08 ...AUTHORS STATE THAT THE GEN BANK ACCESSION CODE FOR 'HIV-1 ENV' 92UG037.8 (HIV1, SAMPLE 037 CLONE 08 FROM UGANDA (HIV192UG037WHO.01083hED) IS U09127

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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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97916
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2010
RadiationMonochromator: CRYOGENICALLY-COOLED SINGLE CRYSTAL SI(111) SIDE BOUNCE MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 3.3→33.44 Å / Num. obs: 8478 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.5
Reflection shellResolution: 3.31→3.45 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.425 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→33.44 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.89 / Occupancy max: 1 / Occupancy min: 1 / SU B: 93.97 / SU ML: 0.654 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.65 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.289 472 5.3 %RANDOM
Rwork0.261 ---
obs0.262 8478 99.5 %-
all-8478 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 130.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å20 Å2
2---0.2 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 3.3→33.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3770 0 0 0 3770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0213865
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7431.9495311
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2595517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17424.538130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.22515522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7141510
X-RAY DIFFRACTIONr_chiral_restr0.0440.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212934
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0451.52595
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.08424148
X-RAY DIFFRACTIONr_scbond_it0.10531270
X-RAY DIFFRACTIONr_scangle_it0.1984.51163
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 31 -
Rwork0.378 640 -
obs--99.85 %
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)
13.9909-0.67980.38024.49471.00797.9495-0.22120.0228-0.5093-0.1534-0.2031-0.00250.5172-0.67450.42420.14880.02420.02280.21860.00380.0458-0.265-7.01611.312
27.5304-1.0434-0.93247.9998-2.6114.5226-0.4241-0.6063-0.28670.22540.2507-0.9696-0.03350.52150.17350.10730.10590.06520.40960.0670.29319.093-23.09415.078
323.6055-4.36072.381829.9277-3.112511.23631.78660.8812-1.0261-3.661-0.3826-1.21032.13680.7269-1.40391.37320.75870.32951.1216-0.27211.705935.465-58.90913.295
422.0589-11.72610.544215.4486-3.33812.1127-0.648-3.0381-1.17241.52692.6639-0.7532-0.0384-0.2352-2.01590.88190.48690.17741.13140.04771.250330.193-50.97526.161
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 157
2X-RAY DIFFRACTION2L4 - 115
3X-RAY DIFFRACTION2H1 - 128
4X-RAY DIFFRACTION3H129 - 226
5X-RAY DIFFRACTION4L116 - 214

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