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- PDB-3uc0: Crystal structure of domain I of the envelope glycoprotein ectodo... -

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Basic information

Entry
Database: PDB / ID: 3uc0
TitleCrystal structure of domain I of the envelope glycoprotein ectodomain from dengue virus serotype 4 in complex with the fab fragment of the chimpanzee monoclonal antibody 5H2
Components
  • Heavy chain, monoclonal antibody 5H2
  • Light chain, monoclonal antibody 5H2
  • envelope protein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / dengue antibody membrane fusion / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


: / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / protein complex oligomerization / monoatomic ion channel activity ...: / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Tick-borne Encephalitis virus Glycoprotein, domain 1 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / : / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain ...Tick-borne Encephalitis virus Glycoprotein, domain 1 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / : / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / Flavivirus envelope glycoprotein E, stem/anchor domain / : / 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. / 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, flavivirus / Flavivirus envelope glycoprotein M / 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
Biological speciesDengue virus 4
Pan troglodytes (chimpanzee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsCockburn, J.J.B. / Stura, E.A. / Navarro-Sanchez, M.E. / Rey, F.A.
CitationJournal: Embo J. / Year: 2012
Title: Structural insights into the neutralization mechanism of a higher primate antibody against dengue virus.
Authors: Cockburn, J.J. / Navarro Sanchez, M.E. / Goncalvez, A.P. / Zaitseva, E. / Stura, E.A. / Kikuti, C.M. / Duquerroy, S. / Dussart, P. / Chernomordik, L.V. / Lai, C.J. / Rey, F.A.
History
DepositionOct 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Database references / Source and taxonomy
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
B: envelope protein
H: Heavy chain, monoclonal antibody 5H2
I: Heavy chain, monoclonal antibody 5H2
L: Light chain, monoclonal antibody 5H2
M: Light chain, monoclonal antibody 5H2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,36619
Polymers132,1216
Non-polymers1,24513
Water6,179343
1
A: envelope protein
H: Heavy chain, monoclonal antibody 5H2
L: Light chain, monoclonal antibody 5H2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4417
Polymers66,0613
Non-polymers3804
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: envelope protein
I: Heavy chain, monoclonal antibody 5H2
M: Light chain, monoclonal antibody 5H2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,92512
Polymers66,0613
Non-polymers8659
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.937, 113.864, 169.583
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein envelope protein


Mass: 17497.500 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 4 / Strain: Myanmar 1976 / Gene: envelope / Plasmid: pT351 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider 2 / References: UniProt: Q91AI1

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Antibody , 2 types, 4 molecules HILM

#2: Antibody Heavy chain, monoclonal antibody 5H2


Mass: 25069.979 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pan troglodytes (chimpanzee) / Plasmid: pCOMB3H / Cell line (production host): ovary (CHO) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Light chain, monoclonal antibody 5H2


Mass: 23493.037 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pan troglodytes (chimpanzee) / Plasmid: pCOMB3H / Cell line (production host): ovary (CHO) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 3 types, 356 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsPROTEIN FRAGMENT COMPRISES UNP RESIDUES 280-329, A GLY-GLY LINKER, UNP RESIDUES 414-469, A THR ...PROTEIN FRAGMENT COMPRISES UNP RESIDUES 280-329, A GLY-GLY LINKER, UNP RESIDUES 414-469, A THR LINKER, UNP RESIDUES 560-577, AND A C-TERMINAL EXPRESSION TAG.

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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: 2.88 Å3/Da / Density % sol: 57.35 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 19, 2009 / Details: Dynamically bendable mirror
RadiationMonochromator: LN2 cooled Fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.71→46.175 Å / Num. all: 41316 / Num. obs: 41316 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 62.45 Å2 / Rsym value: 0.09 / Net I/σ(I): 11.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.71-2.862.30.4291.81188252110.42986.4
2.86-3.033.80.37822175657960.37899.9
3.03-3.244.40.2782.62403354100.27899.9
3.24-3.54.50.1614.52282550390.16199.6
3.5-3.834.50.1037.22108346780.10399.6
3.83-4.284.50.06910.41890942390.06999.8
4.28-4.954.40.04814.21672937910.04899.6
4.95-6.064.40.05113.41404932130.05199.7
6.06-8.574.30.04713.71080524980.04799.2
8.57-46.1754.10.03415.8586914410.03497.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
BUSTER-TNTBUSTER 2.9.3refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
PHASERphasing
BUSTER2.9.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UAJ

3uaj


Resolution: 2.71→46.175 Å / Cor.coef. Fo:Fc: 0.9085 / Cor.coef. Fo:Fc free: 0.8872 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.669 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.721 / SU Rfree Blow DPI: 0.313 / SU Rfree Cruickshank DPI: 0.314 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2524 2073 5.06 %RANDOM
Rwork0.2203 ---
all0.2219 40983 --
obs0.2219 40983 97.63 %-
Displacement parametersBiso max: 157.82 Å2 / Biso mean: 58.4519 Å2 / Biso min: 7.23 Å2
Baniso -1Baniso -2Baniso -3
1--11.0284 Å20 Å20 Å2
2--12.1805 Å20 Å2
3----1.1521 Å2
Refine analyzeLuzzati coordinate error obs: 0.443 Å
Refinement stepCycle: LAST / Resolution: 2.71→46.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8120 0 66 343 8529
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2755SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes167HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1205HARMONIC5
X-RAY DIFFRACTIONt_it8354HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1118SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8634SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8354HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg11376HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion1.84
X-RAY DIFFRACTIONt_other_torsion17.5
LS refinement shellResolution: 2.71→2.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3221 134 5.71 %
Rwork0.2734 2214 -
all0.2761 2348 -
obs-2438 97.63 %
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)
12.2858-0.8369-0.24594.5932-1.01691.49180.0567-0.16550.27810.20630.00640.0957-0.2791-0.067-0.0631-0.11240.0490.0526-0.10990.01080.00575.05882.2775-29.4295
22.1724-0.1721-0.68516.136-1.67053.2820.0155-0.2280.10880.5088-0.0803-0.1764-0.31540.1380.06480.0046-0.0563-0.0071-0.1999-0.0053-0.1906-31.612727.8163-29.558
30.8704-1.55621.19152.9854-0.6994.3906-0.0221-0.0945-0.06940.0938-0.02090.01480.12510.17230.043-0.1261-0.03070.0562-0.05070.0614-0.0329.1764-23.6852-20.316
40.03610.0991.09952.53730.162.00980.05760.0108-0.2682-0.0150.0628-0.01320.2090.1075-0.12040.17950.14630.1129-0.0998-0.0852-0.143211.7939-59.1313-14.9786
51.4027-1.42482.63385.5319-2.66114.8646-0.0214-0.0611-0.04490.0347-0.069-0.220.08060.21640.0903-0.1156-0.00490.0207-0.10630.0594-0.0797-28.77441.4456-21.3424
60.8524-0.9953-0.24940.8194-0.29884.5670.08110.0776-0.32880.1175-0.062-0.0710.02420.2129-0.0191-0.22280.0783-0.14050.069-0.0677-0.0306-30.2706-34.767-15.2063
702.84040.76466.18981.67212.3063-0.03230.2362-0.1040.0152-0.0320.24360.1042-0.25380.0643-0.165-0.0266-0.0173-0.0877-0.04570.0696-4.5658-31.8409-36.176
80.05660.8445-0.31792.5462-1.37682.01440.0421-0.2076-0.1740.0866-0.03570.00720.1656-0.1654-0.00640.2038-0.15190.0899-0.11580.0946-0.1975-4.6869-61.9278-14.8591
90.37911.13240.24374.39170.7060.51930.01580.0212-0.0134-0.172-0.0610.19080.0673-0.04040.04520.03830.01950.0256-0.06310.0204-0.0607-44.1937-5.3941-36.3054
100.8686-0.83221.0512.1769-0.18014.18690.0797-0.2527-0.1690.4881-0.0266-0.15660.3165-0.0604-0.05310.0043-0.085-0.0503-0.07380.0417-0.1118-46.8293-35.8289-14.7458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|51 A|134 - A|144 A|159 - A|192 A|282 - A|296 }A1 - 51
2X-RAY DIFFRACTION1{ A|1 - A|51 A|134 - A|144 A|159 - A|192 A|282 - A|296 }A134 - 144
3X-RAY DIFFRACTION1{ A|1 - A|51 A|134 - A|144 A|159 - A|192 A|282 - A|296 }A159 - 192
4X-RAY DIFFRACTION1{ A|1 - A|51 A|134 - A|144 A|159 - A|192 A|282 - A|296 }A282 - 296
5X-RAY DIFFRACTION2{ B|1 - B|51 B|134 - B|145 B|158 - B|192 B|282 - B|296 }B1 - 51
6X-RAY DIFFRACTION2{ B|1 - B|51 B|134 - B|145 B|158 - B|192 B|282 - B|296 }B134 - 145
7X-RAY DIFFRACTION2{ B|1 - B|51 B|134 - B|145 B|158 - B|192 B|282 - B|296 }B158 - 192
8X-RAY DIFFRACTION2{ B|1 - B|51 B|134 - B|145 B|158 - B|192 B|282 - B|296 }B282 - 296
9X-RAY DIFFRACTION3{ H|1 - H|124 }H1 - 124
10X-RAY DIFFRACTION4{ H|125 - H|136 H|145 - H|223 }H125 - 136
11X-RAY DIFFRACTION4{ H|125 - H|136 H|145 - H|223 }H145 - 223
12X-RAY DIFFRACTION5{ I|1 - I|124 }I1 - 124
13X-RAY DIFFRACTION6{ I|125 - I|138 I|145 - I|223 }I125 - 138
14X-RAY DIFFRACTION6{ I|125 - I|138 I|145 - I|223 }I145 - 223
15X-RAY DIFFRACTION7{ L|2 - L|109 }L2 - 109
16X-RAY DIFFRACTION8{ L|110 - L|210 }L110 - 210
17X-RAY DIFFRACTION9{ M|2 - M|109 }M2 - 109
18X-RAY DIFFRACTION10{ M|110 - M|212 }M110 - 212

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