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- PDB-4ut7: CRYSTAL STRUCTURE OF THE SCFV FRAGMENT OF THE BROADLY NEUTRALIZIN... -

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Entry
Database: PDB / ID: 4ut7
TitleCRYSTAL STRUCTURE OF THE SCFV FRAGMENT OF THE BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11
Components(BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11) x 2
KeywordsIMMUNE SYSTEM / BROADLY NEUTRALIZING ANTIBODY / IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX / VIRAL PROTEIN / MEMBRANE FUSION / CLASS 2 FUSION PROTEIN / DENGUE VIRUS / SCFV FRAGMENT
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M.C. / Rey, F.A.
Citation
Journal: Nature / Year: 2015
Title: Recognition Determinants of Broadly Neutralizing Human Antibodies Against Dengue Viruses.
Authors: Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M. / Kikuti, C.M. / Navarro Sanchez, M.E. / Dejnirattisai, W. / Wongwiwat, W. / Haouz, A. / Girard-Blanc, C. / ...Authors: Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M. / Kikuti, C.M. / Navarro Sanchez, M.E. / Dejnirattisai, W. / Wongwiwat, W. / Haouz, A. / Girard-Blanc, C. / Petres, S. / Shepard, W.E. / Despres, P. / Arenzana-Seisdedos, F. / Dussart, P. / Mongkolsapaya, J. / Screaton, G.R. / Rey, F.A.
#1: Journal: Nat Immunol / Year: 2015
Title: A new class of highly potent, broadly neutralizing antibodies isolated from viremic patients infected with dengue virus.
Authors: Wanwisa Dejnirattisai / Wiyada Wongwiwat / Sunpetchuda Supasa / Xiaokang Zhang / Xinghong Dai / Alexander Rouvinski / Amonrat Jumnainsong / Carolyn Edwards / Nguyen Than Ha Quyen / Thaneeya ...Authors: Wanwisa Dejnirattisai / Wiyada Wongwiwat / Sunpetchuda Supasa / Xiaokang Zhang / Xinghong Dai / Alexander Rouvinski / Amonrat Jumnainsong / Carolyn Edwards / Nguyen Than Ha Quyen / Thaneeya Duangchinda / Jonathan M Grimes / Wen-Yang Tsai / Chih-Yun Lai / Wei-Kung Wang / Prida Malasit / Jeremy Farrar / Cameron P Simmons / Z Hong Zhou / Felix A Rey / Juthathip Mongkolsapaya / Gavin R Screaton /
Abstract: Dengue is a rapidly emerging, mosquito-borne viral infection, with an estimated 400 million infections occurring annually. To gain insight into dengue immunity, we characterized 145 human monoclonal ...Dengue is a rapidly emerging, mosquito-borne viral infection, with an estimated 400 million infections occurring annually. To gain insight into dengue immunity, we characterized 145 human monoclonal antibodies (mAbs) and identified a previously unknown epitope, the envelope dimer epitope (EDE), that bridges two envelope protein subunits that make up the 90 repeating dimers on the mature virion. The mAbs to EDE were broadly reactive across the dengue serocomplex and fully neutralized virus produced in either insect cells or primary human cells, with 50% neutralization in the low picomolar range. Our results provide a path to a subunit vaccine against dengue virus and have implications for the design and monitoring of future vaccine trials in which the induction of antibody to the EDE should be prioritized.
History
DepositionJul 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11
L: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11


Theoretical massNumber of molelcules
Total (without water)31,7022
Polymers31,7022
Non-polymers00
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-11.8 kcal/mol
Surface area11440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.920, 47.670, 90.670
Angle α, β, γ (deg.)90.00, 102.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-2074-

HOH

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Components

#1: Antibody BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11


Mass: 15962.392 Da / Num. of mol.: 1 / Fragment: SCFV HEAVY CHAIN DOMAIN, RESIDUES 1-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: B LYMPHOCYTE / Plasmid: PMT/BIP/V5-HIS / Cell line (production host): SCHNEIDER 2 / Production host: DROSOPHILA MELANOGASTER (fruit fly)
#2: Antibody BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11


Mass: 15740.104 Da / Num. of mol.: 1 / Fragment: SCFV LIGHT CHAIN DOMAIN, RESIDUES 1-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: B LYMPHOCYTE / Plasmid: PMT/BIP/V5-HIS / Cell line (production host): SCHNEIDER 2 / Production host: DROSOPHILA MELANOGASTER (fruit fly)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.21 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: 0.1 M MES 6.5 25% (V/V) PEG 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2013 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.7→29.52 Å / Num. obs: 28835 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.6 / % possible all: 95.5

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FAB A11 FROM THE COMPLEX DENGUE 2 FAB A11

Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.9321 / Cor.coef. Fo:Fc free: 0.9128 / SU R Cruickshank DPI: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.096 / SU Rfree Blow DPI: 0.093 / SU Rfree Cruickshank DPI: 0.091
RfactorNum. reflection% reflectionSelection details
Rfree0.1909 1428 5.02 %RANDOM
Rwork0.1602 ---
obs0.1617 28441 97.92 %-
Displacement parametersBiso mean: 22.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.854 Å20 Å29.9452 Å2
2--5.2199 Å20 Å2
3----3.3659 Å2
Refine analyzeLuzzati coordinate error obs: 0.178 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1927 0 0 213 2140
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012064HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.032818HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d680SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes37HARMONIC2
X-RAY DIFFRACTIONt_gen_planes325HARMONIC5
X-RAY DIFFRACTIONt_it2064HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.95
X-RAY DIFFRACTIONt_other_torsion14.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion263SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2543SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.76 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2677 132 5.06 %
Rwork0.2281 2477 -
all0.2301 2609 -
obs--97.92 %
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)
10.65030.18810.09980.72290.12550.5615-0.00470.0365-0.01780.0064-0.02990.0210.01670.01970.0346-0.0020.0005-0.0241-0.0459-0.0021-0.0094-22.7367-2.186411.1387
20.79790.0375-0.15430.7994-0.07591.7539-0.0033-0.0960.02590.04890.00410.02240.0434-0.042-0.0008-0.0014-0.0135-0.0147-0.01690.0016-0.0298-13.97983.907228.9708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN H
2X-RAY DIFFRACTION2CHAIN L

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