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- PDB-4adg: Crystal structure of the Rubella virus envelope Glycoprotein E1 i... -

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Basic information

Entry
Database: PDB / ID: 4adg
TitleCrystal structure of the Rubella virus envelope Glycoprotein E1 in post-fusion form (crystal form II)
ComponentsE1 ENVELOPE GLYCOPROTEIN
KeywordsVIRAL PROTEIN / MEMBRANE FUSION
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / RNA binding ...T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / RNA binding / metal ion binding / membrane
Similarity search - Function
Rubella membrane glycoprotein E1, domain 3 / Rubella membrane glycoprotein E1, domain 1 / Rubella membrane glycoprotein E1, domain 2 / Rubella capsid / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 / Rubella membrane glycoprotein E1, domain 2 / Rubella membrane glycoprotein E1, domain 3 / Rubella membrane glycoprotein E1, domain 1 / Rubella capsid domain superfamily ...Rubella membrane glycoprotein E1, domain 3 / Rubella membrane glycoprotein E1, domain 1 / Rubella membrane glycoprotein E1, domain 2 / Rubella capsid / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 / Rubella membrane glycoprotein E1, domain 2 / Rubella membrane glycoprotein E1, domain 3 / Rubella membrane glycoprotein E1, domain 1 / Rubella capsid domain superfamily / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 / Rubella capsid protein / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 2-acetamido-2-deoxy-beta-D-galactopyranose / DI(HYDROXYETHYL)ETHER / Structural polyprotein
Similarity search - Component
Biological speciesRUBELLA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsDuBois, R.M. / Vaney, M.C. / Tortorici, M.A. / Al Kurdi, R. / Barba-Spaeth, G. / Rey, F.A.
Citation
Journal: Nature / Year: 2013
Title: Functional and Evolutionary Insight from the Crystal Structure of Rubella Virus Protein E1.
Authors: Dubois, R.M. / Vaney, M.C. / Tortorici, M.A. / Kurdi, R.A. / Barba-Spaeth, G. / Krey, T. / Rey, F.A.
#1: 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. / Roussel, A. / Vigouroux, A. / Reilly, B. / Lepault, J. / Kielian, M. / Rey, F.A.
#2: 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. / Wengler, G. / Rey, F.A.
#3: 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. / Wengler, G. / Wengler, G. / Rey, F.A.
#4: Journal: Embo J. / Year: 2004
Title: Structure of a Flavivirus Envelope Glycoprotein in its Low-Ph-Induced Membrane Fusion Conformation.
Authors: Bressanelli, S. / Stiasny, K. / Allison, S.L. / Stura, E.A. / Duquerroy, S. / Lescar, J. / Heinz, F.X. / Rey, F.A.
History
DepositionDec 26, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.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.conn_type_id / _struct_conn.id / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E1 ENVELOPE GLYCOPROTEIN
B: E1 ENVELOPE GLYCOPROTEIN
C: E1 ENVELOPE GLYCOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,37028
Polymers151,7203
Non-polymers2,65025
Water20,7351151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23660 Å2
ΔGint-97.4 kcal/mol
Surface area49590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.680, 126.550, 130.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein E1 ENVELOPE GLYCOPROTEIN / SPIKE GLYCOPROTEIN E1


Mass: 50573.352 Da / Num. of mol.: 3 / Fragment: ECTODOMAIN, UNP RESIDUES 583-1017
Source method: isolated from a genetically manipulated source
Details: POLYPROTEIN FRAGMENT / Source: (gene. exp.) RUBELLA VIRUS / Strain: M33 / Plasmid: PMT MODIFIED INVITROGEN / Cell line (production host): SCHNEIDER 2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P08563

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Sugars , 2 types, 5 molecules

#2: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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
#7: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE


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

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Non-polymers , 6 types, 1171 molecules

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


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1151 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsCHLORIDE ION (CL): THIS CHLORIDE ION IS LOCATED ON THE PSEUDO 3-FOLD AXIS OF THE E1 TRIMER. CALCIUM ...CHLORIDE ION (CL): THIS CHLORIDE ION IS LOCATED ON THE PSEUDO 3-FOLD AXIS OF THE E1 TRIMER. CALCIUM ION (CA): THE CALCIUM IONS ARE BONDED TO RESIDUES AT THE FUSION LOOPS. GLYCEROL (GOL): E1 PROTEIN WAS CRYSTALLIZED IN PRESENCE OF HIGH CONCENTRATION OF GLYCEROL. N-ACETYL-D-GALACTOSAMINE (NGA): THE THR RESIDUES 429 AND 430 ARE O-GLYCOSYLATED. ACETATE ION (ACT): ACETATE IONS ARE BONDED TO CALCIUM IONS AT THE FUSION LOOPS. N-ACETYL-D-GLUCOSAMINE (NAG): THE ASN RESIDUES 76 AND 177 ARE N-GLYCOSYLATED.
Sequence detailsECTODOMAIN OF E1 FROM AMINO ACIDS FROM 1 (583 IN POLYPROTEIN) TO 436 (1018 IN POLYPROTEIN) WITH THE ...ECTODOMAIN OF E1 FROM AMINO ACIDS FROM 1 (583 IN POLYPROTEIN) TO 436 (1018 IN POLYPROTEIN) WITH THE FOLLOWING SEQUENCE AT THE C-TERMINAL FEDDDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK

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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: 3.03 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growDetails: 2-3% PEG4000, 100MM HEPES PH 7.5-8.0, 30% GLYCEROL. E1 PROTEIN WAS SOAKED WITH 25MM OF GALACTOSE 3-SULFATE (GAL3S, HEAD GROUP OF SULFATIDE) DURING ONE WEEK.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.008
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2008 / Details: DYNAMICALLY BENDABLE
RadiationMonochromator: DOUBLE-CRYSTAL FIXED-EXIT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.18→45.34 Å / Num. obs: 104002 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 12.4 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 19.5
Reflection shellResolution: 2.18→2.3 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.4 / % possible all: 97.4

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AD1

4ad1


Resolution: 2.18→20 Å / Cor.coef. Fo:Fc: 0.9449 / Cor.coef. Fo:Fc free: 0.9335 / Cross valid method: THROUGHOUT / σ(F): 0
Details: DISORDERED REGIONS 210-212 WERE NOT MODELED FOR THE A,B,C CHAINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1934 5179 4.99 %RANDOM
Rwork0.1779 ---
obs0.1786 103791 98.94 %-
Displacement parametersBiso mean: 29.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.3616 Å20 Å20 Å2
2---0.1819 Å20 Å2
3---0.5435 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.18→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9717 0 165 1151 11033
LS refinement shellResolution: 2.18→2.24 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2259 360 4.91 %
Rwork0.2117 6970 -
all0.2124 7330 -
obs--98.94 %
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)
11.9488-0.68890.09622.6301-0.16341.22320.0156-0.0473-0.01090.0133-0.0116-0.10870.13070.2283-0.004-0.05520.0296-0.008-0.0167-0.0053-0.055640.7208-38.4583-28.9434
21.55410.2599-0.03691.1384-0.01671.87110.01930.13340.0933-0.2136-0.0603-0.144-0.00510.10270.041-0.0293-0.00730.0582-0.02370.0205-0.034540.3301-22.2454-43.9921
31.8799-0.31490.00782.29050.51292.03010.00450.1979-0.1772-0.05680.02960.05680.11770.009-0.034-0.0383-0.0240.0007-0.0399-0.0328-0.046125.1616-38.4501-44.6504
40.8974-0.3182-0.72570.43090.56421.0970.0288-0.15980.08880.03520.0041-0.01190.01110.0892-0.0329-0.0478-0.0181-0.0075-0.0168-0.0022-0.04888.7605-11.1445.4952
50.4616-0.5126-0.38750.80540.42760.62090.0373-0.00510.0647-0.06320.0051-0.0819-0.1587-0.0102-0.0425-0.0046-0.0181-0.0089-0.0522-0.0023-0.04019.29788.9108-11.8889
60.792-0.343-0.40780.34910.12660.5035-0.02940.0175-0.07180.04450.03230.09240.0353-0.0568-0.0029-0.0455-0.0130.0063-0.04650.0179-0.009-9.5445-10.001-13.9325
72.5379-0.0642-1.43640.69470.04461.8168-0.01130.04270.1492-0.06580.0784-0.2204-0.00590.1975-0.0671-0.1022-0.04210.0060.0298-0.02080.006147.8681-10.7818-23.5872
80.68280.019-0.14512.06851.6912.93340.0260.0988-0.0472-0.2429-0.01360.0103-0.0769-0.0479-0.01250.0189-0.0031-0.012-0.03460.0154-0.073912.4206-18.6377-51.9358
92.5061-1.93610.05733.569-0.24941.0119-0.02610.0533-0.12030.0354-0.04750.0310.14510.10520.0736-0.02030.0079-0.0024-0.06890.03-0.020620.9918-47.5364-17.4306
100.8048-0.0097-1.18440.05561.17290.08170.0057-0.009-0.0327-0.0490.00770.01620.05990.0117-0.01330.0078-0.0172-0.00960.0565-0.0150.025555.7541-24.9522-35.1689
110.0671-1.5774-0.41440.0804-0.08470.67040.0005-0.0063-0.0463-0.0223-0.0112-0.0599-0.01120.01390.01060.05160.00280.0150.0425-0.00110.004628.0855-29.1809-59.6775
120.0372-0.3899-1.17350.14520.44930.0546-0.00010.0352-0.0115-0.0122-0.0016-0.00820.00290.02940.00160.0433-0.01950.00970.01310.0110.059532.6318-54.1012-32.5009
130.4856-0.45930.364200.329700.00050.04580.0460.00620.01870.0114-0.06750.0338-0.0191-0.0197-0.02720.0417-0.0461-0.01370.020123.16166.3079-8.8742
140-0.23880.01440-0.64930.53390.0039-0.0219-0.0367-0.0244-0.00050.05330.0432-0.1147-0.0034-0.0328-0.0254-0.00410.0131-0.05240.0053-6.6118-6.0163-27.6712
1500.6195-0.15340.43880.012300.009-0.05130.02560.0469-0.01370.01170.02680.02160.00470.00690.04450.0063-0.00230.0237-0.01956.1693-24.98221.9172
160.01760.02250.000300.02990.0236-0.0005-0.00420.00120.0069-0.00140.0009-0.00280.00030.00190.0057-0.0102-0.02510.035-0.0229-0.008247.9119-31.649-20.4044
170.00970.00840.01140.0057-0.00640.0005-0.00010.0005-0.0001-0.00010.0008-0.00250.00020.0023-0.00060.00750.0041-0.00810.00660.00290.025216.731418.9661-10.3111
180.0044-0.0064-0.01040.0186-0.00580.0282-0.0002-0.00150.0045-0.00040.00060.0016-0.004-0.0013-0.00040.03260.00430.00720.00260.0207-0.001533.1794-13.9538-51.2512
190.0220.0136-0.0040.0242-0.00010.00010.0005-0.0021-0.0001-0.0007-0.00030.0049-0.0002-0.0058-0.00020.0008-0.02030.00280.00180.00690.037917.1351-46.3865-37.941
2000.00990.01780.01220.00070.00430-0.0024-0.00120.0010-0.00050.00110.00020.00010.0131-0.0263-0.015-0.00090.00570.0151-16.0396-24.1843-9.4742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:30, 163:200, 318:327)
2X-RAY DIFFRACTION2CHAIN B AND (RESID 1:30, 163:200, 318:327)
3X-RAY DIFFRACTION3CHAIN C AND (RESID 1:30, 163:200, 318:327)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 31:162)
5X-RAY DIFFRACTION5CHAIN B AND (RESID 31:162)
6X-RAY DIFFRACTION6CHAIN C AND (RESID 31:162)
7X-RAY DIFFRACTION7CHAIN A AND (RESID 342:413)
8X-RAY DIFFRACTION8CHAIN B AND (RESID 342:413)
9X-RAY DIFFRACTION9CHAIN C AND (RESID 342:413)
10X-RAY DIFFRACTION10CHAIN A AND (RESID 328:341)
11X-RAY DIFFRACTION11CHAIN B AND (RESID 328:341)
12X-RAY DIFFRACTION12CHAIN C AND (RESID 328:341)
13X-RAY DIFFRACTION13CHAIN A AND (RESID 414:435)
14X-RAY DIFFRACTION14CHAIN B AND (RESID 414:435)
15X-RAY DIFFRACTION15CHAIN C AND (RESID 414:435)
16X-RAY DIFFRACTION16CHAIN A AND RESID 1001
17X-RAY DIFFRACTION17CHAIN A AND RESID 4001
18X-RAY DIFFRACTION18CHAIN B AND RESID 1001
19X-RAY DIFFRACTION19CHAIN C AND RESID 1001
20X-RAY DIFFRACTION20CHAIN C AND RESID 2001

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