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- PDB-4m62: Ontogeny of recognition specificity and functionality for the ant... -

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Basic information

Entry
Database: PDB / ID: 4m62
TitleOntogeny of recognition specificity and functionality for the anti-HIV neutralizing antibody 4E10
Components
  • GEP2 FV heavy chain
  • GEP2 FV light chain
  • T117
KeywordsIMMUNE SYSTEM / GEP / 4E10 germline / Immunoglobulin / Antiboody / HIV
Function / homology
Function and homology information


pentameric IgM immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / glomerular filtration / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation ...pentameric IgM immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / glomerular filtration / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / blood microparticle / Potential therapeutics for SARS / adaptive immune response / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Mannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...Mannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin kappa variable 3-20 / Immunoglobulin kappa variable 3-20
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFinton, K.A.K.
CitationJournal: Plos Pathog. / Year: 2014
Title: Ontogeny of Recognition Specificity and Functionality for the Broadly Neutralizing Anti-HIV Antibody 4E10.
Authors: Finton, K.A. / Friend, D. / Jaffe, J. / Gewe, M. / Holmes, M.A. / Larman, H.B. / Stuart, A. / Larimore, K. / Greenberg, P.D. / Elledge, S.J. / Stamatatos, L. / Strong, R.K.
History
DepositionAug 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: GEP2 FV light chain
H: GEP2 FV heavy chain
M: GEP2 FV light chain
I: GEP2 FV heavy chain
S: T117
T: T117
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,35015
Polymers86,4856
Non-polymers8659
Water12,538696
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9340 Å2
ΔGint-163 kcal/mol
Surface area33080 Å2
MethodPISA
2
S: T117
hetero molecules

T: T117
hetero molecules

L: GEP2 FV light chain
H: GEP2 FV heavy chain
M: GEP2 FV light chain
I: GEP2 FV heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,35015
Polymers86,4856
Non-polymers8659
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation2_555-x+1/2,-y,z+1/21
crystal symmetry operation3_555-x,y+1/2,-z+1/21
identity operation1_555x,y,z1
Buried area9340 Å2
ΔGint-176 kcal/mol
Surface area33070 Å2
MethodPISA
3
L: GEP2 FV light chain
H: GEP2 FV heavy chain
S: T117
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6277
Polymers43,2433
Non-polymers3844
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-80 kcal/mol
Surface area17140 Å2
MethodPISA
4
M: GEP2 FV light chain
I: GEP2 FV heavy chain
T: T117
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7238
Polymers43,2433
Non-polymers4805
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-72 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.880, 103.480, 109.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody GEP2 FV light chain / Ig kappa chain V-III region HIC


Mass: 12211.589 Da / Num. of mol.: 2 / Fragment: UNP residues 21-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P18136, UniProt: P01619*PLUS
#2: Antibody GEP2 FV heavy chain


Mass: 13413.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein T117


Mass: 17617.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 696 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Ac, pH 5.0, 1.6M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 16, 2011
RadiationMonochromator: osmic varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→68.88 Å / Num. all: 72714 / Num. obs: 71260 / % possible obs: 98 %
Reflection shellResolution: 1.8→1.86 Å / % possible all: 98

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.7.0029refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→68.88 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.507 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21608 3668 5.1 %RANDOM
Rwork0.1894 ---
all0.19076 72714 --
obs0.19076 68940 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.525 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→68.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5991 0 45 696 6732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0196248
X-RAY DIFFRACTIONr_bond_other_d0.0050.025760
X-RAY DIFFRACTIONr_angle_refined_deg0.6991.9568537
X-RAY DIFFRACTIONr_angle_other_deg0.5443.00113261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0275809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58624.039255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64115965
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4951532
X-RAY DIFFRACTIONr_chiral_restr0.0510.2959
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0217140
X-RAY DIFFRACTIONr_gen_planes_other00.021420
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 228 -
Rwork0.252 4725 -
obs--91.35 %

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