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- PDB-5aam: Structure of a redesigned cross-reactive antibody to dengue virus... -

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Basic information

Entry
Database: PDB / ID: 5aam
TitleStructure of a redesigned cross-reactive antibody to dengue virus with increased in vivo potency
Components
  • ENVELOPE PROTEIN
  • SCFV513
KeywordsIMMUNE SYSTEM / SCFV DENGUE ANTIBODY ENVELOPE DOMAIN III
Function / homology
Function and homology information


: / viral capsid / clathrin-dependent endocytosis of virus by host cell / protein dimerization activity / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus ...: / viral capsid / clathrin-dependent endocytosis of virus by host cell / protein dimerization activity / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / extracellular region / membrane
Similarity search - Function
Immunoglobulin-like - #350 / Flavivirus capsid protein C superfamily / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide ...Immunoglobulin-like - #350 / Flavivirus capsid protein C superfamily / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
DENGUE VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsWong, Y.H. / Robinson, L.N. / Lescar, J. / Sasisekharan, R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2015
Title: Structure-Guided Design of an Anti-Dengue Antibody Directed to a Non-Immunodominant Epitope.
Authors: Robinson, L.N. / Tharakaraman, K. / Rowley, K.J. / Costa, V.V. / Chan, K.R. / Wong, Y.H. / Ong, L.C. / Tan, H.C. / Koch, T. / Cain, D. / Kirloskar, R. / Viswanathan, K. / Liew, C.W. / ...Authors: Robinson, L.N. / Tharakaraman, K. / Rowley, K.J. / Costa, V.V. / Chan, K.R. / Wong, Y.H. / Ong, L.C. / Tan, H.C. / Koch, T. / Cain, D. / Kirloskar, R. / Viswanathan, K. / Liew, C.W. / Tissire, H. / Ramakrishnan, B. / Myette, J.R. / Babcock, G.J. / Sasisekharan, V. / Alonso, S. / Chen, J. / Lescar, J. / Shriver, Z. / Ooi, E.E. / Sasisekharan, R.
History
DepositionJul 27, 2015Deposition site: PDBE / Processing site: PDBE
SupersessionAug 5, 2015ID: 4UD3
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Jan 10, 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 6, 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
A: SCFV513
B: SCFV513
C: ENVELOPE PROTEIN
J: ENVELOPE PROTEIN


Theoretical massNumber of molelcules
Total (without water)79,9844
Polymers79,9844
Non-polymers00
Water2,288127
1
A: SCFV513
C: ENVELOPE PROTEIN


Theoretical massNumber of molelcules
Total (without water)39,9922
Polymers39,9922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-2.4 kcal/mol
Surface area17890 Å2
MethodPQS
2
B: SCFV513
J: ENVELOPE PROTEIN


Theoretical massNumber of molelcules
Total (without water)39,9922
Polymers39,9922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint0 kcal/mol
Surface area17790 Å2
MethodPQS
Unit cell
Length a, b, c (Å)71.638, 55.891, 87.047
Angle α, β, γ (deg.)90.00, 104.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody SCFV513


Mass: 27299.357 Da / Num. of mol.: 2 / Fragment: SCFV, RESIDUES 2-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli)
#2: Protein ENVELOPE PROTEIN / DENGUE SEROTYPE 4 ENVELOPE PROTEIN DOMAIN III


Mass: 12692.560 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-109
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DENGUE VIRUS / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: U3N5N6, UniProt: Q6YFU0*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.11 Å3/Da / Density % sol: 41.67 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Nov 29, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→47.9 Å / Num. obs: 23183 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 80.51 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.8
Reflection shellResolution: 2.49→2.63 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.15 / Mean I/σ(I) obs: 1.4 / % possible all: 92.3

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.10.0refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UYP

3uyp


Resolution: 2.49→29.55 Å / Cor.coef. Fo:Fc: 0.9426 / Cor.coef. Fo:Fc free: 0.9169 / SU R Cruickshank DPI: 0.766 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.738 / SU Rfree Blow DPI: 0.311 / SU Rfree Cruickshank DPI: 0.317
RfactorNum. reflection% reflectionSelection details
Rfree0.2698 1188 5.12 %RANDOM
Rwork0.2196 ---
obs0.2222 23183 98.05 %-
Displacement parametersBiso mean: 85.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.5462 Å20 Å2-0.5072 Å2
2---1.5469 Å20 Å2
3---2.0931 Å2
Refine analyzeLuzzati coordinate error obs: 0.428 Å
Refinement stepCycle: LAST / Resolution: 2.49→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5010 0 0 127 5137
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015123HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.236945HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1756SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes123HARMONIC2
X-RAY DIFFRACTIONt_gen_planes737HARMONIC5
X-RAY DIFFRACTIONt_it5123HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion21.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion667SEMIHARMONIC5
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_contact5621SEMIHARMONIC4
LS refinement shellResolution: 2.49→2.6 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2778 127 5 %
Rwork0.2197 2411 -
all0.2227 2538 -
obs--98.05 %

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