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- PDB-5ghw: Crystal structure of broad neutralizing antibody 10E8 with long e... -

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Basic information

Entry
Database: PDB / ID: 5ghw
TitleCrystal structure of broad neutralizing antibody 10E8 with long epitope bound
Components
  • Endogenous retrovirus group K member 8 Env polyprotein
  • FAB 10E8 HEAVY CHAIN
  • FAB 10E8 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / BROAD NEUTRALIZING ANTIBODY / RECOMBINANT FAB / EPITOPE / HIV-1 / VIRAL MEMBRANE
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / : / Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity ...virus-mediated perturbation of host defense response => GO:0019049 / : / Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCaaveiro, J.M.M. / Rujas, E. / Morante, K. / Nieva, J.L. / Tsumoto, K.
CitationJournal: Sci Rep / Year: 2016
Title: Structural basis for broad neutralization of HIV-1 through the molecular recognition of 10E8 helical epitope at the membrane interface
Authors: Rujas, E. / Caaveiro, J.M. / Partida-Hanon, A. / Gulzar, N. / Morante, K. / Apellaniz, B. / Garcia-Porras, M. / Bruix, M. / Tsumoto, K. / Scott, J.K. / Jimenez, M.A. / Nieva, J.L.
History
DepositionJun 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: FAB 10E8 HEAVY CHAIN
L: FAB 10E8 LIGHT CHAIN
P: Endogenous retrovirus group K member 8 Env polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,09010
Polymers53,4253
Non-polymers6657
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-80 kcal/mol
Surface area21400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.633, 81.231, 254.216
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Antibody FAB 10E8 HEAVY CHAIN


Mass: 25648.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody FAB 10E8 LIGHT CHAIN


Mass: 23152.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide Endogenous retrovirus group K member 8 Env polyprotein / Endogenous retrovirus group K member 113 Env polyprotein / Endogenous retrovirus group K member 13- ...Endogenous retrovirus group K member 113 Env polyprotein / Endogenous retrovirus group K member 13-1 Env polyprotein / Endogenous retrovirus group K member 18 Env polyprotein / Endogenous retrovirus group K member 19 Env polyprotein / Endogenous retrovirus group K member 21 Env polyprotein / Endogenous retrovirus group K member 24 Env polyprotein / Endogenous retrovirus group K member 25 Env polyprotein / Endogenous retrovirus group K member 6 Env polyprotein / Endogenous retrovirus group K member 7 Env polyprotein / Endogenous retrovirus group K member 9 Env polyprotein / Envelope glycoprotein gp160


Mass: 4623.701 Da / Num. of mol.: 1 / Fragment: UNP residues 674-698 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: G3DED6, UniProt: P04578*PLUS
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT FOR ENTITY 1, GGS RESIDUES AT N-TERMINUS ARE CLONING ARTIFACTS. FOR ENTITY 3, ...AUTHORS STATE THAT FOR ENTITY 1, GGS RESIDUES AT N-TERMINUS ARE CLONING ARTIFACTS. FOR ENTITY 3, THE FOUR LYSINE RESIDUES AT THE N-TERMINUS AND THE FIVE LYSINE RESIDUES AT THE C-TERMINUS ARE SOLUBILIZATION TAGS.

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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: 3.24 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.5 mM DPC 50% MPD 200 mM phosphate 100 mM TRIS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→52.4 Å / Num. obs: 24652 / % possible obs: 90 % / Redundancy: 9.7 % / CC1/2: 0.971 / Rmerge(I) obs: 0.046 / Net I/σ(I): 34
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 8 / % possible all: 56.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLM7.1.0data reduction
Aimless0.3.11data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4g6f

4g6f


Resolution: 2.4→52.4 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.906 / SU B: 11.564 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.321 / ESU R Free: 0.233 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23041 1187 4.8 %RANDOM
Rwork0.19175 ---
obs0.19366 23462 89.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.341 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2--1.6 Å20 Å2
3----2.67 Å2
Refinement stepCycle: 1 / Resolution: 2.4→52.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 35 132 3725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023691
X-RAY DIFFRACTIONr_bond_other_d0.0010.023348
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9535032
X-RAY DIFFRACTIONr_angle_other_deg0.76337742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0525464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44823.497143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00715564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3461518
X-RAY DIFFRACTIONr_chiral_restr0.0790.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214137
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02843
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_it1.1251.4381859
X-RAY DIFFRACTIONr_mcbond_other1.1241.4351858
X-RAY DIFFRACTIONr_mcangle_it1.9972.1442319
X-RAY DIFFRACTIONr_mcangle_other1.9972.1482320
X-RAY DIFFRACTIONr_scbond_it1.311.691832
X-RAY DIFFRACTIONr_scbond_other1.0261.6421805
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.782.4152671
X-RAY DIFFRACTIONr_long_range_B_refined5.37213.0484055
X-RAY DIFFRACTIONr_long_range_B_other5.29412.9464023
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.399→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 51 -
Rwork0.237 1000 -
obs--52.34 %
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)
11.0366-0.1698-0.16191.5826-0.42773.1386-0.0348-0.3134-0.00350.3602-0.0096-0.18890.14860.53610.04440.39960.03760.01750.3952-0.02740.3263-22.06-18.306-26.687
21.98350.2826-0.54431.1556-0.29871.3705-0.00060.0267-0.0338-0.0290.0215-0.02980.04530.0046-0.02090.0036-0.0076-0.00620.0447-0.00110.1905-18.0572-20.1977-61.3001
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 112
2X-RAY DIFFRACTION1L2 - 108
3X-RAY DIFFRACTION2H115 - 215
4X-RAY DIFFRACTION2L111 - 210

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