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- PDB-4m8q: Ontogeny of recognition specificity and functionality for the ant... -

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Basic information

Entry
Database: PDB / ID: 4m8q
TitleOntogeny of recognition specificity and functionality for the anti-HIV neutralizing antibody 4E10
Components
  • 4E10 epitope scaffold T117
  • GEP1 Fv heavy chain
  • GEP1 Fv light chain
KeywordsIMMUNE SYSTEM / HIV / 4E10 / GEP / germline / FV / immunoglobulin / antibody / 4E10 epitope
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 / immunoglobulin complex / Initial triggering of complement / 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 / immunoglobulin complex / Initial triggering of complement / 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 / adaptive immune response / Potential therapeutics for SARS / 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: 2.89 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 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Nov 6, 2024Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GEP1 Fv heavy chain
B: GEP1 Fv light chain
C: 4E10 epitope scaffold T117
H: GEP1 Fv heavy chain
L: GEP1 Fv light chain
S: 4E10 epitope scaffold T117


Theoretical massNumber of molelcules
Total (without water)88,6296
Polymers88,6296
Non-polymers00
Water00
1
A: GEP1 Fv heavy chain
B: GEP1 Fv light chain
S: 4E10 epitope scaffold T117


Theoretical massNumber of molelcules
Total (without water)44,3153
Polymers44,3153
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-25 kcal/mol
Surface area16540 Å2
MethodPISA
2
C: 4E10 epitope scaffold T117
H: GEP1 Fv heavy chain
L: GEP1 Fv light chain


Theoretical massNumber of molelcules
Total (without water)44,3153
Polymers44,3153
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-23 kcal/mol
Surface area16140 Å2
MethodPISA
3
A: GEP1 Fv heavy chain
B: GEP1 Fv light chain
S: 4E10 epitope scaffold T117

C: 4E10 epitope scaffold T117
H: GEP1 Fv heavy chain
L: GEP1 Fv light chain


Theoretical massNumber of molelcules
Total (without water)88,6296
Polymers88,6296
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area8160 Å2
ΔGint-61 kcal/mol
Surface area30780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.561, 77.674, 77.823
Angle α, β, γ (deg.)90.00, 112.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody GEP1 Fv heavy chain


Mass: 13656.305 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)
#2: Antibody GEP1 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
#3: Protein 4E10 epitope scaffold T117


Mass: 18446.848 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)
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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M KCl, 12% w/v PEG 8000, 5% v/v glycerol, pH 7, 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: Apr 17, 2013
RadiationMonochromator: osmic varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.89→24.61 Å / Num. all: 18013 / Num. obs: 17941 / % possible obs: 99.6 %
Reflection shellResolution: 2.89→2.95 Å / % possible all: 97.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→24.61 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.866 / SU B: 50.231 / SU ML: 0.428 / Cross valid method: THROUGHOUT / ESU R: 2.013 / ESU R Free: 0.501 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30168 919 5.1 %RANDOM
Rwork0.26091 ---
all0.26294 17221 --
obs0.26294 17070 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.088 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å2-2.53 Å2
2--2.84 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.89→24.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5424 0 0 0 5424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0195563
X-RAY DIFFRACTIONr_bond_other_d0.0010.024823
X-RAY DIFFRACTIONr_angle_refined_deg0.7331.9417634
X-RAY DIFFRACTIONr_angle_other_deg0.6473.00110987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6865758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.77424.213197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.44115679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.381516
X-RAY DIFFRACTIONr_chiral_restr0.0460.2875
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0216559
X-RAY DIFFRACTIONr_gen_planes_other00.021268
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: 2.89→2.963 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.662 74 -
Rwork0.44 1147 -
obs--92.99 %
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)
13.87010.07630.41765.7089-0.17365.72280.06350.0644-0.22070.30860.0905-0.46950.85740.0664-0.1540.24480.0876-0.15410.2898-0.0860.21710.971-27.383-48.436
22.6837-0.5510.34843.83280.34317.597-0.364-0.77380.50780.33910.5379-0.2779-0.17930.2332-0.17390.2670.2566-0.29470.584-0.27380.36357.701-14.832-32.497
35.09752.30590.53329.23183.39063.59470.1255-0.34790.61920.44180.01060.5803-0.46030.2254-0.13610.3562-0.05570.16770.3675-0.01630.442825.2658.1122.978
45.40380.02320.24836.29891.19533.54260.0475-0.1941-0.03630.4785-0.19570.55450.1601-0.03640.14820.06480.00010.07620.25540.01860.092416.722-17.77813.521
55.6378-0.926-1.32824.57752.18629.3020.47010.72970.1652-0.6483-0.5464-0.0494-0.69560.01670.07630.18430.1575-0.0410.41140.06910.096118.602-12.804-7.138
63.7919-1.0586-1.07485.0826-0.93463.7940.24590.12930.7022-0.96490.2601-0.8549-0.46570.0921-0.5060.3480.0260.23510.3682-0.19680.7511.546-10.251-68.108
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 113
2X-RAY DIFFRACTION2B1 - 105
3X-RAY DIFFRACTION3C13 - 160
4X-RAY DIFFRACTION4H1 - 112
5X-RAY DIFFRACTION5L1 - 105
6X-RAY DIFFRACTION6S8 - 161

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