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- PDB-6ivz: Crystal structure of 5A ScFv complexed with YFV-China sE in postf... -

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Basic information

Entry
Database: PDB / ID: 6ivz
TitleCrystal structure of 5A ScFv complexed with YFV-China sE in postfusion state
Components
  • Envelope protein
  • 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


host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / Flavivirus envelope glycoprotein E, stem/anchor domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 ...Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / Flavivirus envelope glycoprotein E, stem/anchor domain / 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 / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesYellow fever virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 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 1.1Feb 27, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope protein
H: Heavy chain of monoclonal antibody 5A
L: Light chain of monoclonal antibody 5A


Theoretical massNumber of molelcules
Total (without water)70,0163
Polymers70,0163
Non-polymers00
Water2,792155
1
A: Envelope protein
H: Heavy chain of monoclonal antibody 5A
L: Light chain of monoclonal antibody 5A

A: Envelope protein
H: Heavy chain of monoclonal antibody 5A
L: Light chain of monoclonal antibody 5A

A: Envelope protein
H: Heavy chain of monoclonal antibody 5A
L: Light chain of monoclonal antibody 5A


Theoretical massNumber of molelcules
Total (without water)210,0499
Polymers210,0499
Non-polymers00
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Unit cell
Length a, b, c (Å)102.915, 102.915, 364.874
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

21H-217-

HOH

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Components

#1: Protein Envelope protein


Mass: 42950.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yellow fever virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q89292
#2: Antibody Heavy chain of monoclonal antibody 5A


Mass: 13674.211 Da / Num. of mol.: 1
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: 13391.690 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1 M Sodium malonate pH 4.0, 12% w/v Polyethylene glycol 3350

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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: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 25919 / % possible obs: 99.9 % / Redundancy: 14.6 % / Net I/σ(I): 22.8
Reflection shellResolution: 2.4→50 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 2.4→47.391 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.24
RfactorNum. reflection% reflection
Rfree0.2564 1333 5.14 %
Rwork0.2099 --
obs0.2123 25919 87.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→47.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4745 0 0 155 4900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054859
X-RAY DIFFRACTIONf_angle_d0.856590
X-RAY DIFFRACTIONf_dihedral_angle_d14.4161745
X-RAY DIFFRACTIONf_chiral_restr0.037738
X-RAY DIFFRACTIONf_plane_restr0.003842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3998-2.48560.3301620.2755934X-RAY DIFFRACTION34
2.4856-2.58510.3279910.2991413X-RAY DIFFRACTION51
2.5851-2.70280.36981170.29072413X-RAY DIFFRACTION86
2.7028-2.84520.32211620.27662759X-RAY DIFFRACTION100
2.8452-3.02350.32921520.25792790X-RAY DIFFRACTION100
3.0235-3.25690.28631360.24742813X-RAY DIFFRACTION100
3.2569-3.58450.27731500.22272802X-RAY DIFFRACTION100
3.5845-4.10290.24011560.18822833X-RAY DIFFRACTION100
4.1029-5.16830.19781480.15322849X-RAY DIFFRACTION100
5.1683-47.39980.19991590.17972980X-RAY DIFFRACTION100
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)
10.0826-0.00640.05790.2051-0.31440.2397-0.0011-0.02210.04540.03070.02920.1046-0.0662-0.07520.00580.12680.00820.0240.1208-0.0230.1064-13.0197-51.54426.6375
20.13960.02110.1060.04860.04840.10230.01280.17940.1368-0.3217-0.0527-0.041-0.22770.3187-0.00290.3595-0.04030.01380.2660.08070.2673-1.8603-26.1846-52.3541
30.1624-0.0089-0.16410.0589-0.05740.3119-0.0691-0.05030.48360.0750.04130.0727-0.31040.0680.0190.26780.0411-0.07910.158-0.00670.4507-5.2233-17.4148-33.0771
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain H
3X-RAY DIFFRACTION3chain L

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