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- PDB-5cin: Crystal Structure of non-neutralizing version of 4E10 (DeltaLoop)... -

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Basic information

Entry
Database: PDB / ID: 5cin
TitleCrystal Structure of non-neutralizing version of 4E10 (DeltaLoop) with epitope bound
Components
  • FAB 4E10 HEAVY CHAIN
  • FAB 4E10 LIGHT CHAIN
  • Peptide from MPER region of HIV-1 ENV
KeywordsIMMUNE SYSTEM / BROADLY NEUTRALIZING ANTIBODY / RECOMBINANT FAB / ENV-PEPTIDE / HIV-1 / EPITOPE
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / 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 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCaaveiro, J.M.M. / Rujas, E. / Nieva, J.L. / Tsumoto, K.
Funding support United States, Japan, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI097051-01 United States
Japan Society for the Promotion of Science25249115 Japan
CitationJournal: J.Virol. / Year: 2015
Title: Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10
Authors: Rujas, E. / Gulzar, N. / Morante, K. / Tsumoto, K. / Scott, J.K. / Nieva, J.L. / Caaveiro, J.M.M.
History
DepositionJul 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 23, 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 4E10 LIGHT CHAIN
P: Peptide from MPER region of HIV-1 ENV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0328
Polymers48,6283
Non-polymers4045
Water10,521584
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.520, 44.660, 85.340
Angle α, β, γ (deg.)90.00, 113.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide Peptide from MPER region of HIV-1 ENV


Mass: 2187.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS

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Antibody , 2 types, 2 molecules HL

#1: Antibody FAB 4E10 HEAVY CHAIN


Mass: 23334.219 Da / Num. of mol.: 1 / Mutation: W100S, W100(B)null, L100(C)null
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 4E10 LIGHT CHAIN


Mass: 23106.541 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

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Non-polymers , 3 types, 589 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.86 Å3/Da / Density % sol: 56.99 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM TRSI-HCl, 200mM Ammonium acetate, 30% PEG 4,000

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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 315 / Detector: CCD / Date: May 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→36.1 Å / Num. obs: 59239 / % possible obs: 98.3 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 12.5
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 3.3 / % possible all: 88.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WY7

4wy7


Resolution: 1.7→36.1 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.616 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17798 2379 4 %RANDOM
Rwork0.14754 ---
obs0.14873 56860 98.22 %-
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: 25.702 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20.3 Å2
2---0.38 Å20 Å2
3---0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.7→36.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3377 0 25 584 3986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023622
X-RAY DIFFRACTIONr_bond_other_d0.0010.023354
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9564960
X-RAY DIFFRACTIONr_angle_other_deg0.7937777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6635.021485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15923.793145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.30915577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8481521
X-RAY DIFFRACTIONr_chiral_restr0.0930.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214159
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02832
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_it1.7782.3461827
X-RAY DIFFRACTIONr_mcbond_other1.7772.3431826
X-RAY DIFFRACTIONr_mcangle_it2.7363.5042288
X-RAY DIFFRACTIONr_mcangle_other2.7383.5082289
X-RAY DIFFRACTIONr_scbond_it2.4472.5821795
X-RAY DIFFRACTIONr_scbond_other2.4452.5821795
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8093.7542652
X-RAY DIFFRACTIONr_long_range_B_refined6.18220.5814404
X-RAY DIFFRACTIONr_long_range_B_other5.83519.4324068
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 148 -
Rwork0.199 3494 -
obs--82.38 %

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