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- PDB-3n41: Crystal structure of the mature envelope glycoprotein complex (sp... -

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Basic information

Entry
Database: PDB / ID: 3n41
TitleCrystal structure of the mature envelope glycoprotein complex (spontaneous cleavage) of Chikungunya virus.
Components
  • E1 envelope glycoprotein
  • E2 envelope glycoprotein
  • E3 envelope glycoprotein
KeywordsVIRAL PROTEIN / IMMATURE HETERODIMER / ALPHAVIRUS / RECEPTOR BINDING / MEMBRANE FUSION
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis ...T=4 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Helix Hairpins - #2230 / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein, A domain / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Helix Hairpins - #2230 / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein, A domain / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Helix Hairpins / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesChikungunya virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsVoss, J. / Vaney, M.C. / Duquerroy, S. / Rey, F.A.
Citation
Journal: Nature / Year: 2010
Title: Glycoprotein organization of Chikungunya virus particles revealed by X-ray crystallography.
Authors: James E Voss / Marie-Christine Vaney / Stéphane Duquerroy / Clemens Vonrhein / Christine Girard-Blanc / Elodie Crublet / Andrew Thompson / Gérard Bricogne / Félix A Rey /
Abstract: Chikungunya virus (CHIKV) is an emerging mosquito-borne alphavirus that has caused widespread outbreaks of debilitating human disease in the past five years. CHIKV invasion of susceptible cells is ...Chikungunya virus (CHIKV) is an emerging mosquito-borne alphavirus that has caused widespread outbreaks of debilitating human disease in the past five years. CHIKV invasion of susceptible cells is mediated by two viral glycoproteins, E1 and E2, which carry the main antigenic determinants and form an icosahedral shell at the virion surface. Glycoprotein E2, derived from furin cleavage of the p62 precursor into E3 and E2, is responsible for receptor binding, and E1 for membrane fusion. In the context of a concerted multidisciplinary effort to understand the biology of CHIKV, here we report the crystal structures of the precursor p62-E1 heterodimer and of the mature E3-E2-E1 glycoprotein complexes. The resulting atomic models allow the synthesis of a wealth of genetic, biochemical, immunological and electron microscopy data accumulated over the years on alphaviruses in general. This combination yields a detailed picture of the functional architecture of the 25 MDa alphavirus surface glycoprotein shell. Together with the accompanying report on the structure of the Sindbis virus E2-E1 heterodimer at acidic pH (ref. 3), this work also provides new insight into the acid-triggered conformational change on the virus particle and its inbuilt inhibition mechanism in the immature complex.
#1: Journal: Structure / Year: 2006
Title: Structure and interactions at the viral surface of the envelope protein E1 of Semliki Forest virus.
Authors: Roussel, A. / Lescar, J. / Vaney, M.C. / Wengler, G. / Rey, F.A.
#2: Journal: Nature / Year: 2004
Title: Conformational change and protein-protein interactions of the fusion protein of Semliki Forest virus.
Authors: Gibbons, D.L. / Vaney, M.C. / Roussel, A. / Vigouroux, A. / Reilly, B. / Lepault, J. / Kielian, M. / Rey, F.A.
#3: Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: The Fusion glycoprotein shell of Semliki Forest virus: an icosahedral assembly primed for fusogenic activation at endosomal pH.
Authors: Lescar, J. / Roussel, A. / Wien, M.W. / Navaza, J. / Fuller, S.D. / Wengler, G. / Rey, F.A.
#4: Journal: To be Published
Title: Structural Changes of Envelope Proteins During Alphavirus Fusion.
Authors: Li, L. / Jose, J. / Xiang, Y. / Kuhn, R.J. / Rossmann, M.G.
History
DepositionMay 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: E3 envelope glycoprotein
B: E2 envelope glycoprotein
F: E1 envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0735
Polymers98,4283
Non-polymers6462
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-12 kcal/mol
Surface area36670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.240, 99.610, 107.100
Angle α, β, γ (deg.)90.00, 102.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 3 molecules ABF

#1: Protein E3 envelope glycoprotein


Mass: 7470.737 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 266-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Strain: 05-115 / Plasmid: pMRBiP/V5 HisA / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila Melanogaster (fruit fly) / References: UniProt: Q1H8W5
#2: Protein E2 envelope glycoprotein


Mass: 40600.785 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 330-667
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Strain: 05-115 / Plasmid: pMRBiP/V5 HisA / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila Melanogaster (fruit fly) / References: UniProt: Q1H8W5
#3: Protein E1 envelope glycoprotein


Mass: 50356.223 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 810-1190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Strain: 05-115 / Plasmid: pMRBiP/V5 HisA / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila Melanogaster (fruit fly) / References: UniProt: Q1H8W5

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Sugars , 2 types, 2 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 23 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 293 K / pH: 7
Details: 8-12% PEG4K, 100mM NaAcetate, 100mM Hepes pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9795
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2009 / Details: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 20262 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 76.7 Å2 / Rsym value: 0.073 / Net I/σ(I): 12.2
Reflection shellResolution: 3→3.17 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.475 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.9.3refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: P62E1 ENVELOPE GLYCOPROTEINS FROM CHIKUNGUNYA VIRUS

Resolution: 3.01→50 Å / Cor.coef. Fo:Fc: 0.845 / Cor.coef. Fo:Fc free: 0.82 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1027 5.09 %RANDOM
Rwork0.252 ---
obs0.253 20166 98.3 %-
all-20166 --
Displacement parametersBiso mean: 89.18 Å2
Baniso -1Baniso -2Baniso -3
1-5.1013 Å20 Å2-24.6049 Å2
2---9.1578 Å20 Å2
3---4.0565 Å2
Refine analyzeLuzzati coordinate error obs: 0.79 Å
Refinement stepCycle: LAST / Resolution: 3.01→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5998 0 42 23 6063
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0076228HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.968503HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2056SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes145HARMONIC2
X-RAY DIFFRACTIONt_gen_planes907HARMONIC5
X-RAY DIFFRACTIONt_it6228HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.78
X-RAY DIFFRACTIONt_other_torsion19.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion839SEMIHARMONIC5
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_contact6339SEMIHARMONIC4
LS refinement shellResolution: 3.01→3.17 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3244 140 4.98 %
Rwork0.2786 2673 -
all0.2808 2813 -
obs--98.32 %
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)
1-0.3978-1.10910.64074.0238-0.24421.98950.0018-0.04060.06750.05410.0190.0186-0.0753-0.0199-0.02080.03930.01660.0102-0.1429-0.13840.157-17.5647-2.6166-2.7615
23.5442-0.5755-1.33961.13280.45384.748-0.056-0.1607-0.0367-0.01360.0411-0.01770.12990.28480.0149-0.12930.0124-0.0573-0.2063-0.0376-0.062-5.0016-26.1782-9.757
31.9639-0.39280.19281.31182.03752.87620.0045-0.0716-0.03140.0797-0.00050.0370.0136-0.0424-0.0040.0890.02950.00910.06060.0576-0.0545-26.4238-25.906318.4808
42.9945-1.6489-1.37621.8582.51851.00180.00370.1477-0.0463-0.16130.0247-0.00210.02520.0658-0.02840.02410.13870.07750.0807-0.1202-0.08779.433-38.455-49.3014
5-0.0667-0.16791.75670.81151.57544.16680.01610.05240.0501-0.10280.0242-0.0885-0.10140.1459-0.04030.0626-0.12020.07160.1164-0.0238-0.22331.2624-14.4637-66.2302
62.59911.6622-0.172800.8334.05410.0010.08250.058-0.06910.0480.08220.0537-0.1341-0.049-0.0135-0.0133-0.01050.0943-0.0435-0.155-15.9845-25.3039-37.2184
75.99990.8065-1.75861.43750.08091.4334-0.0023-0.0101-0.02440.07240.02060.07960.0813-0.0986-0.0183-0.14750.01280.0043-0.14630.07780.1379-28.2636-31.4161-7.3728
80.07620.2690.14990.37130.1550.16030.00180.0002-0.00260.0102-0.00120.00260.0011-0.0034-0.00070.0457-0.0207-0.00470.0194-0.0056-0.000610.9977-0.9201-84.1371
91.5018-1.0862-1.49430.05940.49480.6073-0.0086-0.01370.01090.0072-0.0135-0.01860.020.0290.0221-0.03410.04580.05260.1214-0.0166-0.033922.5555-20.0918-80.9018
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|5:59}
2X-RAY DIFFRACTION2{B|5:169 233:268}
3X-RAY DIFFRACTION3{B|170:232}
4X-RAY DIFFRACTION4{B|269:342}
5X-RAY DIFFRACTION5{F|0-39 127:171 255:281}
6X-RAY DIFFRACTION6{F|40:51 111:126 172:216 238:254}
7X-RAY DIFFRACTION7{F|52:110 217:237}
8X-RAY DIFFRACTION8{F|282:293}
9X-RAY DIFFRACTION9{F|294:381}

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