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- PDB-4wy7: Crystal structure of recombinant 4E10 expressed in Escherichia co... -

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Basic information

Entry
Database: PDB / ID: 4wy7
TitleCrystal structure of recombinant 4E10 expressed in Escherichia coli with epitope bound
Components
  • Envelope glycoprotein gp160
  • Fab 4E10 Heavy chain
  • Fab 4E10Light chain
KeywordsIMMUNE SYSTEM / broad neutralizing antobody / recombinant Fab / epitope
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / 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
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
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRujas, E. / Morante, K. / Tsumoto, K. / Nieva, J.L. / Caaveiro, J.M.M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The Atomic Structure of the HIV-1 gp41 Transmembrane Domain and Its Connection to the Immunogenic Membrane-proximal External Region.
Authors: Apellaniz, B. / Rujas, E. / Serrano, S. / Morante, K. / Tsumoto, K. / Caaveiro, J.M. / Jimenez, M.A. / Nieva, J.L.
History
DepositionNov 16, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Fab 4E10 Heavy chain
L: Fab 4E10Light chain
P: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6555
Polymers49,4703
Non-polymers1842
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-36 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.300, 44.580, 85.400
Angle α, β, γ (deg.)90.00, 113.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Fab 4E10 Heavy chain


Mass: 23990.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-Duet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T7 Shuffle
#2: Antibody Fab 4E10Light chain


Mass: 23292.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-Duet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T7 Shuffle
#3: Protein/peptide Envelope glycoprotein gp160 / Env polyprotein


Mass: 2187.582 Da / Num. of mol.: 1 / Fragment: UNP residues 662-674
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Strain: isolate WMJ22 / Gene: env / Production host: synthetic construct (others) / References: UniProt: P05880
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM sodium acetate 30% PEG 8,000 100 mM sodium cacodylate Protein was prepared in PBS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→44.7 Å / Num. obs: 30114 / % possible obs: 94.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 14
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.3 / % possible all: 76.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLM7.1.0data reduction
SCALA3.3.21data scaling
PHASER2.5.6phasing
Coot0.7 and 0.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FX7

2fx7


Resolution: 2.1→44.7 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.171 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 1530 5.1 %RANDOM
Rwork0.16169 ---
obs0.16397 28584 93.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20.5 Å2
2---1.13 Å20 Å2
3---0.97 Å2
Refinement stepCycle: 1 / Resolution: 2.1→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 12 304 3722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023577
X-RAY DIFFRACTIONr_bond_other_d0.0010.023309
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9464885
X-RAY DIFFRACTIONr_angle_other_deg0.7643.0017651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0445.043467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36223.846143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81115564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9331518
X-RAY DIFFRACTIONr_chiral_restr0.0880.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214066
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02823
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_it1.963.0141806
X-RAY DIFFRACTIONr_mcbond_other1.9593.0111805
X-RAY DIFFRACTIONr_mcangle_it2.9594.5032256
X-RAY DIFFRACTIONr_mcangle_other2.9594.5062257
X-RAY DIFFRACTIONr_scbond_it2.543.3121771
X-RAY DIFFRACTIONr_scbond_other2.543.3121771
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9494.852619
X-RAY DIFFRACTIONr_long_range_B_refined5.94825.1454091
X-RAY DIFFRACTIONr_long_range_B_other5.84724.9583992
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 87 -
Rwork0.174 1521 -
obs--68.25 %

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