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- PDB-4ffz: Crystal Structure of DENV1-E111 fab fragment bound to DENV-1 DIII... -

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Basic information

Entry
Database: PDB / ID: 4ffz
TitleCrystal Structure of DENV1-E111 fab fragment bound to DENV-1 DIII (Western Pacific-74 strain).
Components
  • DENV1-E111 fab fragment (heavy chain)
  • DENV1-E111 fab fragment (light chain)
  • Envelope protein E
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / structural genomics / antibody fab fragment / Flavivirus / Dengue virus / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / immunoglobulin-like domain / viral envelope protein / virion / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / endoplasmic reticulum membrane / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Immunoglobulin-like - #350 / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus ...Immunoglobulin-like - #350 / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Envelope protein E
Similarity search - Component
Biological speciesDengue virus 1
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8 Å
AuthorsAustin, S.K. / Nelson, C.A. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Plos Pathog. / Year: 2012
Title: Structural Basis of Differential Neutralization of DENV-1 Genotypes by an Antibody that Recognizes a Cryptic Epitope.
Authors: Austin, S.K. / Dowd, K.A. / Shrestha, B. / Nelson, C.A. / Edeling, M.A. / Johnson, S. / Pierson, T.C. / Diamond, M.S. / Fremont, D.H.
History
DepositionJun 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Envelope protein E
L: DENV1-E111 fab fragment (light chain)
H: DENV1-E111 fab fragment (heavy chain)
X: Envelope protein E
Y: DENV1-E111 fab fragment (light chain)
Z: DENV1-E111 fab fragment (heavy chain)


Theoretical massNumber of molelcules
Total (without water)119,0596
Polymers119,0596
Non-polymers00
Water0
1
A: Envelope protein E
L: DENV1-E111 fab fragment (light chain)
H: DENV1-E111 fab fragment (heavy chain)


Theoretical massNumber of molelcules
Total (without water)59,5303
Polymers59,5303
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-34 kcal/mol
Surface area23410 Å2
MethodPISA
2
X: Envelope protein E
Y: DENV1-E111 fab fragment (light chain)
Z: DENV1-E111 fab fragment (heavy chain)


Theoretical massNumber of molelcules
Total (without water)59,5303
Polymers59,5303
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-34 kcal/mol
Surface area23200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.865, 52.013, 136.402
Angle α, β, γ (deg.)90.000, 107.490, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21Y
12L
22Y
13H
23Z
14A
24X

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'L' and (resseq 1:106)) or (chain 'H' and (resseq 1:112))L0
211(chain 'Y' and (resseq 1:106)) or (chain 'Z' and (resseq 1:112))Y0
112chain 'L' and (resseq 107:212)L107 - 212
212chain 'Y' and (resseq 107:212)Y107 - 212
113chain 'H' and (resseq 113:212)H113 - 212
213chain 'Z' and (resseq 113:212)Z113 - 212
114chain 'A'A299 - 395
214chain 'X'X299 - 395

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Envelope protein E /


Mass: 11999.771 Da / Num. of mol.: 2 / Fragment: UNP residues 573-679
Source method: isolated from a genetically manipulated source
Details: refolded / Source: (gene. exp.) Dengue virus 1 / Strain: Nauru/West Pac/1974 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P17763, UniProt: Q88640*PLUS
#2: Antibody DENV1-E111 fab fragment (light chain)


Mass: 23797.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody DENV1-E111 fab fragment (heavy chain)


Mass: 23732.730 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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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: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 6000, 0.1M MES, 1% glycerol., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.007 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.305
ReflectionResolution: 3.8→50 Å / Num. obs: 11029 / % possible obs: 98 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.12 / Χ2: 1.022 / Net I/σ(I): 9.74
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
3.8-3.9740.5141.9113841.04498.6
3.97-4.184.10.35513521.02998.2
4.18-4.444.10.23213561.03598.3
4.44-4.794.10.18613651.00898.8
4.79-5.274.10.15313761.00298.5
5.27-6.034.10.14413891.04898.3
6.03-7.594.10.11213961.04997.8
7.59-503.80.05614110.95295.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.7.3phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AEH,4FFY

4aeh

4ffy


Resolution: 3.8→43.448 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 1.36 / Phase error: 35.3 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2776 563 5.12 %
Rwork0.2366 --
obs0.2375 10996 97.44 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 84.262 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 245.83 Å2 / Biso mean: 158.043 Å2 / Biso min: 93.55 Å2
Baniso -1Baniso -2Baniso -3
1-6.9365 Å20 Å29.6015 Å2
2--39.7128 Å20 Å2
3----46.6493 Å2
Refinement stepCycle: LAST / Resolution: 3.8→43.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8180 0 0 0 8180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038395
X-RAY DIFFRACTIONf_angle_d0.85911424
X-RAY DIFFRACTIONf_chiral_restr0.0621278
X-RAY DIFFRACTIONf_plane_restr0.0041456
X-RAY DIFFRACTIONf_dihedral_angle_d11.3392994
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11L1794X-RAY DIFFRACTIONPOSITIONAL0.016
12Y1794X-RAY DIFFRACTIONPOSITIONAL0.016
21L831X-RAY DIFFRACTIONPOSITIONAL0.039
22Y831X-RAY DIFFRACTIONPOSITIONAL0.039
31H720X-RAY DIFFRACTIONPOSITIONAL0.023
32Z720X-RAY DIFFRACTIONPOSITIONAL0.023
41A745X-RAY DIFFRACTIONPOSITIONAL0.014
42X745X-RAY DIFFRACTIONPOSITIONAL0.014
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.8004-4.18250.28611380.30882527266591
4.1825-4.78690.27291410.25662606274794
4.7869-6.02780.27091360.23022630276694
6.0278-40.62540.27751380.20552675281392

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