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

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Basic information

Entry
Database: PDB / ID: 5aaw
TitleStructure of a redesigned cross-reactive antibody to dengue virus with increased in vivo potency
Components
  • DENGUE SEROTYPE 4 ENVELOPE PROTEIN DOMAIN 3
  • SCFV513
KeywordsVIRAL PROTEIN / 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
Biological speciesMUS MUSCULUS (house mouse)
DENGUE VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å
AuthorsWong, Y. / Robinson, L. / 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 30, 2015Deposition site: PDBE / Processing site: PDBE
SupersessionSep 30, 2015ID: 4UDZ
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: 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 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
A: SCFV513
B: SCFV513
C: DENGUE SEROTYPE 4 ENVELOPE PROTEIN DOMAIN 3
D: SCFV513
E: DENGUE SEROTYPE 4 ENVELOPE PROTEIN DOMAIN 3
F: SCFV513
G: DENGUE SEROTYPE 4 ENVELOPE PROTEIN DOMAIN 3
H: SCFV513
I: DENGUE SEROTYPE 4 ENVELOPE PROTEIN DOMAIN 3
J: DENGUE SEROTYPE 4 ENVELOPE PROTEIN DOMAIN 3
K: SCFV513
L: DENGUE SEROTYPE 4 ENVELOPE PROTEIN DOMAIN 3


Theoretical massNumber of molelcules
Total (without water)240,72012
Polymers240,72012
Non-polymers00
Water72140
1
A: SCFV513
C: DENGUE SEROTYPE 4 ENVELOPE PROTEIN DOMAIN 3


Theoretical massNumber of molelcules
Total (without water)40,1202
Polymers40,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint0.5 kcal/mol
Surface area17300 Å2
MethodPQS
2
B: SCFV513
J: DENGUE SEROTYPE 4 ENVELOPE PROTEIN DOMAIN 3


Theoretical massNumber of molelcules
Total (without water)40,1202
Polymers40,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint0.5 kcal/mol
Surface area17160 Å2
MethodPQS
3
D: SCFV513
E: DENGUE SEROTYPE 4 ENVELOPE PROTEIN DOMAIN 3


Theoretical massNumber of molelcules
Total (without water)40,1202
Polymers40,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint0.3 kcal/mol
Surface area17090 Å2
MethodPQS
4
F: SCFV513
G: DENGUE SEROTYPE 4 ENVELOPE PROTEIN DOMAIN 3


Theoretical massNumber of molelcules
Total (without water)40,1202
Polymers40,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint1 kcal/mol
Surface area17290 Å2
MethodPQS
5
H: SCFV513
I: DENGUE SEROTYPE 4 ENVELOPE PROTEIN DOMAIN 3


Theoretical massNumber of molelcules
Total (without water)40,1202
Polymers40,1202
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint1 kcal/mol
Surface area17310 Å2
MethodPQS
6
K: SCFV513
L: DENGUE SEROTYPE 4 ENVELOPE PROTEIN DOMAIN 3


Theoretical massNumber of molelcules
Total (without water)40,1202
Polymers40,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint1.8 kcal/mol
Surface area17160 Å2
MethodPQS
Unit cell
Length a, b, c (Å)87.110, 131.670, 176.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9985, 0.04857, 0.02545), (0.04779, -0.9984, 0.03034), (0.02688, -0.02907, -0.99922)-2.16, 1.28, 1.57
2given(0.9985, 0.04857, 0.02545), (0.04779, -0.9984, 0.03034), (0.02688, -0.02907, -0.99922)-2.16, 1.28, 1.57
3given(0.99118, 0.0773, 0.10764), (0.07845, -0.9969, -0.0065), (0.10681, 0.01489, -0.99417)4.12651, 0.003, -56.46233
4given(0.99118, 0.0773, 0.10764), (0.07845, -0.9969, -0.0065), (0.10681, 0.01489, -0.99417)4.12651, 0.003, -56.46233
5given(-0.98637, -0.14917, -0.06944), (0.14832, -0.98879, 0.01721), (-0.07123, 0.00668, 0.99744)37.65792, 2.50799, -31.39086
6given(-0.98637, -0.14917, -0.06944), (0.14832, -0.98879, 0.01721), (-0.07123, 0.00668, 0.99744)37.65792, 2.50799, -31.39086
7given(-0.994, -0.072, -0.077), (0.064, -0.992, 0.109), (-0.084, 0.104, 0.991)32.27873, 3.75382, 26.27884
8given(-0.994, -0.072, -0.077), (0.064, -0.992, 0.109), (-0.084, 0.104, 0.991)32.27873, 3.75382, 26.27884
9given(-1, 0.023, -0.021), (0.024, 0.999, -0.045), (0.02, -0.045, -0.999)34.60756, -0.40744, -29.97834
10given(-1, 0.023, -0.021), (0.024, 0.999, -0.045), (0.02, -0.045, -0.999)34.60756, -0.40744, -29.97834

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Components

#1: Antibody
SCFV513


Mass: 27427.488 Da / Num. of mol.: 6 / Fragment: SCFV
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli)
#2: Protein
DENGUE SEROTYPE 4 ENVELOPE PROTEIN DOMAIN 3


Mass: 12692.560 Da / Num. of mol.: 6 / Fragment: D3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DENGUE VIRUS / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q6YFR6*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.1 Å3/Da / Density % sol: 41.48 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.27→105.53 Å / Num. obs: 31554 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 4.9
Reflection shellResolution: 3.27→3.45 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UD3

4ud3
PDB Unreleased entry


Resolution: 3.27→48.75 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.844 / SU B: 35.888 / SU ML: 0.547 / Cross valid method: THROUGHOUT / ESU R Free: 0.618 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26258 1618 5.1 %RANDOM
Rwork0.22661 ---
obs0.22847 30349 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.975 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 3.27→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15068 0 0 40 15108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215436
X-RAY DIFFRACTIONr_bond_other_d0.0030.0214398
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.94620933
X-RAY DIFFRACTIONr_angle_other_deg2.24333217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7251929
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.53324.288667
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.929152607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9691589
X-RAY DIFFRACTIONr_chiral_restr0.0850.22287
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117511
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023498
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_it2.8575.0627761
X-RAY DIFFRACTIONr_mcbond_other2.855.0627760
X-RAY DIFFRACTIONr_mcangle_it4.8727.5789675
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8035.3287675
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: 3.273→3.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 118 -
Rwork0.316 2209 -
obs--99.36 %

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