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- PDB-7n05: Crystal structure of the F240 antibody fragment bound to the HIV-... -

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Basic information

Entry
Database: PDB / ID: 7n05
TitleCrystal structure of the F240 antibody fragment bound to the HIV-1 gp41 immunodominant region
Components
  • Fab F240 heavy chain
  • Fab F240 light chain
  • HIV-1 gp41 immunodominant region
KeywordsIMMUNE SYSTEM / antibody / Fab / anti-HIV / gp41 / immunodominant domain
Function / homologyACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
HIV-1 06TG.HT008 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCook, J.D. / Lee, J.E.
Funding support Canada, 5items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-115066 Canada
Canadian Institutes of Health Research (CIHR)PJT-173301 Canada
Ontario Early Researcher AwardsER-13-09-116 Canada
Canada Research Chairs950-231672 Canada
Canada Foundation for Innovation Canada
CitationJournal: Commun Biol / Year: 2022
Title: Conformational plasticity of the HIV-1 gp41 immunodominant region is recognized by multiple non-neutralizing antibodies.
Authors: Cook, J.D. / Khondker, A. / Lee, J.E.
History
DepositionMay 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab F240 heavy chain
L: Fab F240 light chain
E: HIV-1 gp41 immunodominant region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8776
Polymers52,6343
Non-polymers2433
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-32 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.072, 168.748, 78.367
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein/peptide , 1 types, 1 molecules E

#3: Protein/peptide HIV-1 gp41 immunodominant region


Mass: 1616.836 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HIV-1 06TG.HT008 (virus)

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Antibody , 2 types, 2 molecules HL

#1: Antibody Fab F240 heavy chain


Mass: 26653.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#2: Antibody Fab F240 light chain


Mass: 24363.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 432 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.89 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.17 M ammonium acetate, 0.085 M sodium citrate-HCl, pH 5.6, 25.5% (w/v) PEG 4000, and 15% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 5, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→46.07 Å / Num. obs: 66334 / % possible obs: 97.4 % / Redundancy: 13.8 % / Biso Wilson estimate: 24.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.035 / Rrim(I) all: 0.131 / Net I/σ(I): 16.1 / Num. measured all: 916192
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.739.92.9432663927010.2190.9733.1060.877.7
9-46.07120.031667555810.0090.03255.599.6

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7N04

7n04


Resolution: 1.7→45.697 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 20.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2038 2000 3.02 %
Rwork0.1722 64223 -
obs0.1732 66223 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.24 Å2 / Biso mean: 34.1563 Å2 / Biso min: 14.61 Å2
Refinement stepCycle: final / Resolution: 1.7→45.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3482 0 34 429 3945
Biso mean--37.82 41.99 -
Num. residues----455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013596
X-RAY DIFFRACTIONf_angle_d1.0664896
X-RAY DIFFRACTIONf_chiral_restr0.062547
X-RAY DIFFRACTIONf_plane_restr0.007626
X-RAY DIFFRACTIONf_dihedral_angle_d12.4132121
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.74250.37341110.3679355677
1.7425-1.78970.3921240.3374398986
1.7897-1.84230.33471400.2896449996
1.8423-1.90180.24511440.2374636100
1.9018-1.96980.24571460.20664668100
1.9698-2.04860.22921460.18864672100
2.0486-2.14190.19831450.17554683100
2.1419-2.25480.21741470.1724703100
2.2548-2.39610.21631460.16744717100
2.3961-2.5810.21131470.17274726100
2.581-2.84070.20821480.16644738100
2.8407-3.25170.16121490.15874773100
3.2517-4.09640.18151500.14134822100
4.0964-45.6970.18061570.15315041100
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)
12.2535-2.0137-2.31053.6843.4556.27810.01320.0952-0.2367-0.0844-0.21020.3783-0.0674-0.30430.1690.1271-0.02740.03620.1645-0.03610.243-21.42919.751-25.818
22.7558-0.5714-0.82052.79281.22623.2514-0.213-0.4321-0.37310.48980.09030.16510.37290.24120.07260.29130.05970.09880.24010.05570.2611-16.49616.777-17.596
30.8768-0.32530.12121.34050.11560.592-0.0994-0.09360.05880.0628-0.01040.0428-0.063-0.04510.11610.15710.0087-0.01980.1944-0.02280.1316-17.38139.421-20.721
45.22623.2881-1.46146.3821-3.53615.0787-0.0768-0.02120.65250.07380.28270.6168-0.367-0.5599-0.15140.20850.043-0.08470.2813-0.03940.2859-27.42454.792-23.453
51.8789-2.09681.97447.5435-1.74125.0154-0.0461-0.05270.07510.42890.0494-0.3946-0.220.06950.0180.0902-0.0117-0.02780.2267-0.02630.23796.48633.033-23.185
63.9778-1.28840.20263.1734-0.32632.6804-0.0465-0.2479-0.33390.4581-0.0617-0.69830.16140.09520.04590.18690.03060.02430.23260.03640.28818.46416.431-23.834
77.4163-3.9005-3.74424.90414.55197.4903-0.03870.16320.0959-0.1612-0.15190.1709-0.1994-0.25910.21250.1406-0.01340.01840.1215-0.00890.1653-4.04927.746-29.034
80.8536-0.308-0.052.46410.43980.9245-0.0159-0.00260.0357-0.0449-0.0847-0.2174-0.0034-0.01940.06470.1254-0.0105-0.01390.1789-0.00080.1456-1.43834.577-24.712
94.198-2.4538-3.46641.74742.15064.3491-0.2183-0.13440.12540.2275-0.0079-0.0659-0.08570.01820.18330.2871-0.0079-0.08320.2158-0.07080.2551-6.41154.292-12.723
101.3504-0.417-0.75872.13541.29983.6192-0.1068-0.16670.23010.2071-0.1036-0.1404-0.3378-0.1173-0.0180.26070.0287-0.12790.2316-0.07660.2258-8.81856.761-9.324
115.75412.3922-1.91573.78963.1016.07490.18890.46410.2855-0.1569-0.14990.1678-0.23050.1151-0.04330.24040.06480.02730.1826-0.06540.2735-5.4457.975-34.026
121.1741.97931.89014.6653.65653.20990.04140.938-1.402-0.4335-0.146-1.00051.18471.0056-0.38290.45270.15710.14390.3913-0.07620.43142.5986.307-36.781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:33 )H1 - 33
2X-RAY DIFFRACTION2( CHAIN H AND RESID 34:87 )H34 - 87
3X-RAY DIFFRACTION3( CHAIN H AND RESID 88:188 )H88 - 188
4X-RAY DIFFRACTION4( CHAIN H AND RESID 189:213 )H189 - 213
5X-RAY DIFFRACTION5( CHAIN L AND RESID 2:18 )L2 - 18
6X-RAY DIFFRACTION6( CHAIN L AND RESID 19:32 )L19 - 32
7X-RAY DIFFRACTION7( CHAIN L AND RESID 33:48 )L33 - 48
8X-RAY DIFFRACTION8( CHAIN L AND RESID 49:128 )L49 - 128
9X-RAY DIFFRACTION9( CHAIN L AND RESID 129:150 )L129 - 150
10X-RAY DIFFRACTION10( CHAIN L AND RESID 151:212 )L151 - 212
11X-RAY DIFFRACTION11( CHAIN E AND RESID 596:603 )E596 - 603
12X-RAY DIFFRACTION12( CHAIN E AND RESID 604:610 )E604 - 610

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