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- PDB-6iw2: Crystal structure of 5A ScFv in complex with YFV-17D sE in prefus... -

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Basic information

Entry
Database: PDB / ID: 6iw2
TitleCrystal structure of 5A ScFv in complex with YFV-17D sE in prefusion state
Components
  • Envelope protein E
  • Heavy chain of monoclonal antibody 5A
  • Light chain of monoclonal antibody 5A
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Yellow fever virus / Neutralizing monoclonal antibody / Envelope protein / Flavivirus / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / GTP binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Viral Envelope Glycoprotein, domain 2 / Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus ...Viral Envelope Glycoprotein, domain 2 / Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / 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. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / 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 NS3 helicase, C-terminal helical 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 / 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesYellow fever virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsLu, X.S. / Xiao, H.X. / Li, S.H. / Pang, X.F.
CitationJournal: Cell Rep / Year: 2019
Title: Double Lock of a Human Neutralizing and Protective Monoclonal Antibody Targeting the Yellow Fever Virus Envelope.
Authors: Lu, X. / Xiao, H. / Li, S. / Pang, X. / Song, J. / Liu, S. / Cheng, H. / Li, Y. / Wang, X. / Huang, C. / Guo, T. / Ter Meulen, J. / Daffis, S. / Yan, J. / Dai, L. / Rao, Z. / Klenk, H.D. / ...Authors: Lu, X. / Xiao, H. / Li, S. / Pang, X. / Song, J. / Liu, S. / Cheng, H. / Li, Y. / Wang, X. / Huang, C. / Guo, T. / Ter Meulen, J. / Daffis, S. / Yan, J. / Dai, L. / Rao, Z. / Klenk, H.D. / Qi, J. / Shi, Y. / Gao, G.F.
History
DepositionDec 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope protein E
B: Heavy chain of monoclonal antibody 5A
C: Light chain of monoclonal antibody 5A
D: Envelope protein E
E: Heavy chain of monoclonal antibody 5A
F: Light chain of monoclonal antibody 5A
G: Envelope protein E
H: Heavy chain of monoclonal antibody 5A
I: Light chain of monoclonal antibody 5A
J: Envelope protein E
K: Heavy chain of monoclonal antibody 5A
L: Light chain of monoclonal antibody 5A
M: Envelope protein E
N: Heavy chain of monoclonal antibody 5A
O: Light chain of monoclonal antibody 5A
P: Envelope protein E
Q: Heavy chain of monoclonal antibody 5A
R: Light chain of monoclonal antibody 5A


Theoretical massNumber of molelcules
Total (without water)410,86818
Polymers410,86818
Non-polymers00
Water00
1
A: Envelope protein E
B: Heavy chain of monoclonal antibody 5A
C: Light chain of monoclonal antibody 5A
D: Envelope protein E
E: Heavy chain of monoclonal antibody 5A
F: Light chain of monoclonal antibody 5A


Theoretical massNumber of molelcules
Total (without water)136,9566
Polymers136,9566
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Envelope protein E
H: Heavy chain of monoclonal antibody 5A
I: Light chain of monoclonal antibody 5A
J: Envelope protein E
K: Heavy chain of monoclonal antibody 5A
L: Light chain of monoclonal antibody 5A


Theoretical massNumber of molelcules
Total (without water)136,9566
Polymers136,9566
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
M: Envelope protein E
N: Heavy chain of monoclonal antibody 5A
O: Light chain of monoclonal antibody 5A
P: Envelope protein E
Q: Heavy chain of monoclonal antibody 5A
R: Light chain of monoclonal antibody 5A


Theoretical massNumber of molelcules
Total (without water)136,9566
Polymers136,9566
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.967, 99.244, 123.099
Angle α, β, γ (deg.)96.39, 94.90, 100.36
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Envelope protein E


Mass: 43234.848 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yellow fever virus (strain 17D vaccine)
Strain: 17D vaccine / Production host: Escherichia coli (E. coli) / References: UniProt: P03314
#2: Antibody
Heavy chain of monoclonal antibody 5A


Mass: 13543.016 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody
Light chain of monoclonal antibody 5A


Mass: 11700.068 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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: 2.8 Å3/Da / Density % sol: 56.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M magnesium chloride, 0.1 M Tris pH 8.0, 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 84055 / % possible obs: 98.1 % / Redundancy: 3.5 % / Net I/σ(I): 7
Reflection shellResolution: 2.9→48.7 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 2.9→48.695 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.91
RfactorNum. reflection% reflection
Rfree0.272 4170 4.96 %
Rwork0.2375 --
obs0.2392 84055 85.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→48.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28492 0 0 0 28492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00829210
X-RAY DIFFRACTIONf_angle_d0.89539616
X-RAY DIFFRACTIONf_dihedral_angle_d13.83810479
X-RAY DIFFRACTIONf_chiral_restr0.0364439
X-RAY DIFFRACTIONf_plane_restr0.0045039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8917-2.92450.4509600.33971363X-RAY DIFFRACTION42
2.9245-2.95890.3564730.33861569X-RAY DIFFRACTION52
2.9589-2.9950.3996890.33911769X-RAY DIFFRACTION55
2.995-3.03290.3495940.32521766X-RAY DIFFRACTION58
3.0329-3.07280.35371130.31921919X-RAY DIFFRACTION62
3.0728-3.11490.34841190.3212015X-RAY DIFFRACTION65
3.1149-3.15940.32491100.31472171X-RAY DIFFRACTION70
3.1594-3.20650.35081140.31592328X-RAY DIFFRACTION73
3.2065-3.25660.36591320.31892360X-RAY DIFFRACTION76
3.2566-3.310.37441410.32752548X-RAY DIFFRACTION80
3.31-3.36710.33921350.31032575X-RAY DIFFRACTION85
3.3671-3.42830.3471440.29292768X-RAY DIFFRACTION87
3.4283-3.49420.32281550.28882806X-RAY DIFFRACTION91
3.4942-3.56550.30271710.27562978X-RAY DIFFRACTION94
3.5655-3.6430.29511610.27482947X-RAY DIFFRACTION96
3.643-3.72770.35271350.27712994X-RAY DIFFRACTION95
3.7277-3.82090.29431420.25993076X-RAY DIFFRACTION97
3.8209-3.92420.28831740.25473022X-RAY DIFFRACTION97
3.9242-4.03960.26141950.23073033X-RAY DIFFRACTION98
4.0396-4.16990.24531660.21423087X-RAY DIFFRACTION98
4.1699-4.31890.24051580.21033016X-RAY DIFFRACTION98
4.3189-4.49170.21691490.19433102X-RAY DIFFRACTION99
4.4917-4.69590.20711430.18183090X-RAY DIFFRACTION98
4.6959-4.94330.18011450.17623103X-RAY DIFFRACTION99
4.9433-5.25270.19481600.18393095X-RAY DIFFRACTION99
5.2527-5.65770.23741610.20173093X-RAY DIFFRACTION99
5.6577-6.2260.25371540.21923113X-RAY DIFFRACTION99
6.226-7.12450.28181420.22763079X-RAY DIFFRACTION98
7.1245-8.9670.2731500.19673097X-RAY DIFFRACTION99
8.967-48.7020.2411850.20883003X-RAY DIFFRACTION97

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