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- PDB-4bz1: Structure of dengue virus EDIII in complex with Fab 3e31 -

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Basic information

Entry
Database: PDB / ID: 4bz1
TitleStructure of dengue virus EDIII in complex with Fab 3e31
Components
  • ENVELOPE PROTEINViral envelope
  • FAB 3E31 HEAVY CHAIN
  • FAB 3E31 LIGHT CHAIN
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX / FUSION LOOP / VIRION
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / protein dimerization activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
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 ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesDENGUE VIRUS 4
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLi, J. / Watterson, D. / Chang, C.W. / Li, X.Q. / Ericsson, D.J. / Qiu, L.W. / Cai, J.P. / Chen, J. / Fry, S.R. / Cooper, M.A. ...Li, J. / Watterson, D. / Chang, C.W. / Li, X.Q. / Ericsson, D.J. / Qiu, L.W. / Cai, J.P. / Chen, J. / Fry, S.R. / Cooper, M.A. / Che, X.Y. / Young, P.R. / Kobe, B.
CitationJournal: To be Published
Title: Structure of Dengue Virus Ediii in Complex with Fab 3E31
Authors: Li, J. / Watterson, D. / Chang, C.W. / Li, X.Q. / Ericsson, D.J. / Qiu, L.W. / Cai, J.P. / Chen, J. / Fry, S.R. / Cooper, M.A. / Che, X.Y. / Young, P.R. / Kobe, B.
History
DepositionJul 23, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENVELOPE PROTEIN
H: FAB 3E31 HEAVY CHAIN
L: FAB 3E31 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,95312
Polymers58,5413
Non-polymers4129
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-34.8 kcal/mol
Surface area29380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.802, 107.009, 134.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ENVELOPE PROTEIN / Viral envelope


Mass: 11175.703 Da / Num. of mol.: 1 / Fragment: DOMAIN 3, RESIDUES 301-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DENGUE VIRUS 4 / Production host: KOMAGATAELLA PASTORIS GS115 (fungus) / References: UniProt: Q7TGC7

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Antibody , 2 types, 2 molecules HL

#2: Antibody FAB 3E31 HEAVY CHAIN


Mass: 23263.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Strain: BALB/C
#3: Antibody FAB 3E31 LIGHT CHAIN


Mass: 24101.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Strain: BALB/C

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Non-polymers , 5 types, 111 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.39 Å3/Da / Density % sol: 48.6 % / Description: NONE
Crystal growDetails: 0.01 M ZINC CHLORIDE, 0.1 M SODIUM ACETATE PH 5.0, 20% (W/V) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95369
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.15→57.06 Å / Num. obs: 32253 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 14 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 19.54
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 2.1 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R29

2r29


Resolution: 2.15→53.504 Å / SU ML: 0.31 / σ(F): 1.46 / Phase error: 26.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2546 1633 5.1 %
Rwork0.2234 --
obs0.225 32246 99.89 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.6 Å2
Refinement stepCycle: LAST / Resolution: 2.15→53.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4040 0 19 102 4161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034168
X-RAY DIFFRACTIONf_angle_d0.7395659
X-RAY DIFFRACTIONf_dihedral_angle_d12.8571491
X-RAY DIFFRACTIONf_chiral_restr0.044634
X-RAY DIFFRACTIONf_plane_restr0.003712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.21330.35361260.30272490X-RAY DIFFRACTION99
2.2133-2.28470.38721320.33982489X-RAY DIFFRACTION100
2.2847-2.36640.31511390.28122514X-RAY DIFFRACTION100
2.3664-2.46110.28751410.27492508X-RAY DIFFRACTION100
2.4611-2.57320.30051300.26962502X-RAY DIFFRACTION100
2.5732-2.70880.34541370.27172536X-RAY DIFFRACTION100
2.7088-2.87850.2811310.25652541X-RAY DIFFRACTION100
2.8785-3.10070.28971340.24912549X-RAY DIFFRACTION100
3.1007-3.41270.27521470.23452540X-RAY DIFFRACTION100
3.4127-3.90640.21551310.20262585X-RAY DIFFRACTION100
3.9064-4.92120.19751370.16852612X-RAY DIFFRACTION100
4.9212-53.5210.2291480.20072747X-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)
12.5432-2.0651-0.69395.90230.01292.86-0.15140.31330.0669-0.9421-0.1208-1.5559-0.02120.35570.20690.43010.06410.21230.32440.04180.7621-20.520525.16664.2944
24.65730.95192.02268.8595-1.42478.0869-0.02690.1668-0.3413-0.2657-0.2204-0.80150.5945-0.10230.20660.34640.06360.12060.2120.00870.3867-25.357716.105911.1038
35.6935-3.2680.52737.4916-0.74733.42440.01120.4708-0.1472-0.5118-0.2661-0.8040.52110.19970.21820.37420.01140.1340.2455-0.02920.4012-25.024521.56677.2803
42.60140.76970.23014.24431.44883.70220.1468-0.3509-0.13290.2052-0.0777-0.15150.2237-0.0017-0.05670.1575-0.0103-0.0120.2885-0.02270.1837-31.911850.511.9118
52.13991.7310.83478.07822.28624.60780.17470.0580.12010.18390.06970.0571-0.01290.0908-0.24910.11870.02660.00590.3197-0.02240.2221-31.095554.2110.4272
61.5343-1.4608-0.5673.24250.35342.0538-0.6267-0.48530.34151.94110.3615-1.0898-0.06060.28510.24571.07970.17-0.42950.5034-0.07260.7212-19.304921.539629.7453
70.6301-1.0145-0.79784.95112.04520.3853-0.1265-0.0860.15581.20340.1011-0.58520.3922-0.0480.04110.4017-0.0212-0.10870.42620.02080.272-34.100143.702424.4413
86.299-2.90832.03525.7313-0.58944.2385-0.0011-0.5646-0.18140.83640.04470.08940.2777-0.4052-0.04940.3287-0.0948-0.02110.3528-0.02890.2605-41.855654.034125.4683
96.0310.6706-3.25041.995-4.4499.6670.8881.0036-0.3672-0.3443-0.31340.32830.5288-1.8455-0.41710.90190.1189-0.24651.0403-0.10660.6102-30.9656-9.03198.3188
108.22911.2271-0.93912.26431.35717.0218-0.29430.63610.2638-0.8412-0.1769-0.0250.4057-1.1060.4590.74360.07950.03040.5212-0.04370.5174-26.9761-2.889611.6079
112.0283-0.9292-3.94017.67351.57566.24920.0144-0.9877-0.47771.7264-0.1302-1.30091.22980.91290.07641.2152-0.0343-0.25210.65320.06810.6494-16.4658-13.013719.2574
121.99922.45352.06746.5831.7521.94591.046-0.14610.47970.4644-0.47850.91850.7536-1.5876-0.66510.62040.01420.10731.0182-0.08550.5415-33.7208-3.369114.9298
137.69871.98741.2856.64561.84526.93390.40150.8021-0.29850.5555-0.0798-0.77570.94140.0624-0.31640.68290.08820.00950.405-0.02390.3855-20.984-7.960713.4786
148.22412.94324.81412.1328-0.52817.10510.66190.78051.65640.227-0.5852-0.38470.0430.7233-0.06260.65080.16230.15860.5604-0.04340.8164-11.7257-4.554211.8429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN H AND (RESID 1 THROUGH 32 )
2X-RAY DIFFRACTION2CHAIN H AND (RESID 33 THROUGH 64 )
3X-RAY DIFFRACTION3CHAIN H AND (RESID 65 THROUGH 115 )
4X-RAY DIFFRACTION4CHAIN H AND (RESID 116 THROUGH 172 )
5X-RAY DIFFRACTION5CHAIN H AND (RESID 173 THROUGH 217 )
6X-RAY DIFFRACTION6CHAIN L AND (RESID 1 THROUGH 96 )
7X-RAY DIFFRACTION7CHAIN L AND (RESID 97 THROUGH 156 )
8X-RAY DIFFRACTION8CHAIN L AND (RESID 157 THROUGH 218 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 301 THROUGH 310 )
10X-RAY DIFFRACTION10CHAIN A AND (RESID 311 THROUGH 336 )
11X-RAY DIFFRACTION11CHAIN A AND (RESID 337 THROUGH 350 )
12X-RAY DIFFRACTION12CHAIN A AND (RESID 351 THROUGH 363 )
13X-RAY DIFFRACTION13CHAIN A AND (RESID 364 THROUGH 386 )
14X-RAY DIFFRACTION14CHAIN A AND (RESID 387 THROUGH 396 )

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