PDB-3n43: Crystal structures of the mature envelope glycoprotein complex (t...

Basic information

• Entry: Database: PDB / ID: 3n43
• Title: Crystal structures of the mature envelope glycoprotein complex (trypsin cleavage) of Chikungunya virus.

Components

• E1 envelope glycoprotein
• E2 envelope glycoprotein
• E3 envelope glycoprotein

• Keywords: VIRAL PROTEIN / IMMATURE HETERODIMER / ALPHAVIRUS / RECEPTOR BINDING / MEMBRANE FUSION
• Function / homology: Alphavirus E2 glycoprotein / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin E-set / Peptidase S1, PA clan / Alphavirus E1 glycoprotein / Alphavirus E3 spike glycoprotein / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Alphavirus core protein / host cell membrane / viral capsid / fusion of virus membrane with host endosome membrane / host cell cytoplasm / virion attachment to host cell / virion membrane / structural molecule activity / serine-type endopeptidase activity / integral component of membrane / identical protein binding / Structural polyprotein
• Specimen source: Chikungunya virus (Chikungunya)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / SAD / 2.58 Å resolution
• Authors: Voss, 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 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.

• Validation Report: SummaryFull reportAbout validation report

Date

Deposition: May 21, 2010 / Release: Dec 1, 2010

Revision	Date	Data content type	Group	Provider	Type
1.0	Dec 1, 2010	Structure model		repository	Initial release
1.1	Jul 13, 2011	Structure model	Version format compliance

Assembly

Deposited unit

A: E3 envelope glycoprotein

B: E2 envelope glycoprotein

F: E1 envelope glycoprotein

hetero molecules

Summary:

• 99.2 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	99,150	7
Polyers	98,428	3
Non-polymers	723	4
Water	2,756	153

1

Summary:

• idetical with deposited unit
• defined by author&software
• Download structure data

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area (Å2)	7810
ΔGint (kcal/M)	-20
Surface area (Å2)	37100
Method	PISA

Unit cell

γ

α

β

Length a, b, c (Å)	58.406, 90.812, 179.450
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P 21 21 21

Components

Protein/peptide , 3 types, 3 molecules A B F

#1: Protein/peptide

A E3 envelope glycoprotein

Details:

Mass: 7470.737 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 268-318 / Source: (gene. exp.) Chikungunya virus (Chikungunya) / Strain: 05-115 / Plasmid name: pMRBiP/V5 HisA / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila Melanogaster (fruit fly) / References: UniProt:Q1H8W5

#2: Protein/peptide

B E2 envelope glycoprotein

Details:

Mass: 40600.785 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 332-667 / Source: (gene. exp.) Chikungunya virus (Chikungunya) / Strain: 05-115 / Plasmid name: pMRBiP/V5 HisA / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila Melanogaster (fruit fly) / References: UniProt:Q1H8W5

#3: Protein/peptide

F E1 envelope glycoprotein

Details:

Mass: 50356.223 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 810-1200 / Source: (gene. exp.) Chikungunya virus (Chikungunya) / Strain: 05-115 / Plasmid name: pMRBiP/V5 HisA / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila Melanogaster (fruit fly) / References: UniProt:Q1H8W5

Non-polymers , 4 types, 157 molecules

#4: Chemical

B-2001 F-1001 ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE

Details:

Mass: 221.208 Da / Num. of mol.: 2 / Formula: C₈H₁₅NO₆ / N-Acetylglucosamine

#5: Chemical

F-1002 ChemComp-NDG / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Details:

Mass: 221.208 Da / Num. of mol.: 1 / Formula: C₈H₁₅NO₆

#6: Chemical

F-452 ChemComp-ACT / ACETATE ION

Details:

Mass: 59.044 Da / Num. of mol.: 1 / Formula: C₂H₃O₂ / Acetate

#7: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 153 / Formula: H₂O / Water

Details

• Sequence details: THE RESIDUES ARE PART OF THE LINKER BETWEEN P AND F CHAINS. LINKER WAS CLEAVED BY CHYMOTRYPSIN BEFORE CRYSTALLIZATION.

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 2.42 / Density percent sol: 49.12
• Crystal grow: Temp: 293 K / pH: 7; Details: 8-12% PEG4K, 100mM NaAcetate, 100mM Hepes pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Data collection

• Diffraction: Mean temperature: 110 kelvins
• Source: Source: SYNCHROTRON / Type: ESRF BEAMLINE ID23-2 / Synchrotron site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
• Detector: Type: MARMOSAIC 225 mm CCD; Details: ONE PAIR OF (300X40X15) MM3 LONG PT COATED SI MIRROR, 260MM USABLE, IN A KIRKPATRICK-BAEZ GEOMETRY; Detector: CCD / Collection date: Sep 19, 2009
• Radiation: Monochromator: SI(111) / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.8726 Å / Relative weight: 1
• Reflection: B iso Wilson estimate: 47.71 Ų / D resolution high: 2.58 Å / D resolution low: 89.72 Å / Observed criterion sigma I: 0 / Rsym value: 0.129 / NetI over sigmaI: 8.8 / Redundancy: 3.9 / Percent possible obs: 97.7
• Reflection shell: Highest resolution: 2.6 Å / Lowest resolution: 2.73 Å / MeanI over sigI obs: 2 / Rsym value: 0.31 / Redundancy: 2 / Percent possible all: 93.1

Processing

Software

Name	Version	Classification
DNA		data collection
PHASER		phasing
BUSTER	2.9.3	refinement
XDS		data reduction
SCALA		data scaling

Refine

Method to determine structure: SAD
Starting model: P62E1 ENVELOPE GLYCOPROTEINS FROM CHIKUNGUNYA VIRUS

Correlation coeff Fo to Fc: 0.867 / Correlation coeff Fo to Fc free: 0.862 / Overall SU R Cruickshank DPI: 0.693 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: Engh & Huber

• Displacement parameters: B iso mean: 45.49 Ų / Aniso B11: 0.5439 Ų / Aniso B12: 0 Ų / Aniso B13: 0 Ų / Aniso B22: 11.5921 Ų / Aniso B23: 0 Ų / Aniso B33: -12.136 Ų
• Least-squares process: R factor R free: 0.257 / R factor R work: 0.245 / R factor obs: 0.246 / Highest resolution: 2.58 Å / Lowest resolution: 44 Å / Number reflection R free: 1525 / Number reflection all: 35436 / Number reflection obs: 30189 / Percent reflection R free: 5.05 / Percent reflection obs: 97.8
• Refine analyze: Luzzati coordinate error obs: 0.48 Å
• Refine hist #LAST: Highest resolution: 2.58 Å / Lowest resolution: 44 Å
• Number of atoms included #LAST: Protein: 6039 / Nucleic acid: 0 / Ligand: 46 / Solvent: 153 / Total: 6238

Refine LS restraints

Refine ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.007	6261	HARMONIC	2.000
X-RAY DIFFRACTION	t_angle_deg	0.91	8545	HARMONIC	2.000
X-RAY DIFFRACTION	t_dihedral_angle_d		2066	SINUSOIDAL	2.000
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		147	HARMONIC	2.000
X-RAY DIFFRACTION	t_gen_planes		910	HARMONIC	5.000
X-RAY DIFFRACTION	t_it		6261	HARMONIC	20.000
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	1.590
X-RAY DIFFRACTION	t_other_torsion	17.960
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		842	SEMIHARMONIC	5.000
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		6330	SEMIHARMONIC	4.000

• Refine LS shell: Highest resolution: 2.58 Å / R factor R free: 0.2536 / R factor R work: 0.2698 / R factor all: 0.2689 / Lowest resolution: 2.67 Å / Number reflection R free: 145 / Number reflection R work: 2323 / Number reflection all: 2468 / Total number of bins used: 15 / Percent reflection R free: 5.88 / Percent reflection obs: 97.78

Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

ID	L11	L12	L13	L22	L23	L33	S11	S12	S13	S21	S22	S23	S31	S32	S33	T11	T12	T13	T22	T23	T33	Origin x	Origin y	Origin z
1	1.2667	-0.7923	1.0870	1.1776	-0.7007	0.0000	0.0051	0.0283	0.0181	-0.0293	-0.0161	0.0400	-0.0057	-0.0401	0.0109	-0.1070	0.0107	-0.0979	-0.0075	0.0390	0.1889	-56.3158	-13.8192	-35.7624
2	2.0346	1.9389	0.4117	4.9002	1.5176	0.1571	-0.0117	-0.0540	0.0891	0.5497	-0.1307	0.4031	0.0960	-0.0266	0.1424	0.0498	-0.0514	0.1550	-0.2137	-0.0112	-0.1004	-35.9239	-15.9275	-17.5114
3	7.2212	0.5172	-1.4219	0.2403	0.6699	0.7213	-0.0007	0.1029	-0.1125	-0.0848	0.0021	-0.0461	0.1839	-0.0084	-0.0014	-0.0922	-0.1148	0.0136	-0.0602	0.0546	0.0305	-50.1099	-45.3983	-31.6891
4	3.0112	-1.0622	1.6850	1.4803	2.5250	2.9473	0.0064	-0.1696	0.0136	0.1867	-0.0069	-0.0692	-0.0056	0.0715	0.0005	-0.0331	-0.0711	-0.1466	-0.1118	0.0121	0.0100	-4.1135	13.2130	-9.1537
5	0.4955	1.1986	0.2126	2.1520	0.1376	0.6653	-0.0178	0.0914	-0.0720	-0.0754	0.0063	0.0603	-0.0048	-0.0059	0.0114	-0.0485	-0.0168	-0.0164	-0.0314	0.0170	0.0253	-12.7745	36.1377	-28.2726
6	0.0605	1.4476	-0.7231	5.3882	1.4223	3.4389	0.0233	0.0396	0.0148	-0.0655	-0.0044	-0.1009	-0.1068	-0.0101	-0.0189	-0.1481	0.0020	-0.0477	-0.0783	0.0024	0.0403	-18.3978	1.4250	-33.9163
7	1.5988	1.1292	1.1059	3.1269	1.1503	1.2325	0.0198	-0.0535	-0.0363	-0.0710	0.0170	0.0516	-0.0229	-0.0277	-0.0368	-0.0846	0.0063	0.0243	-0.0295	-0.0127	-0.0402	-30.1594	-28.9365	-36.7474
8	0.0003	-0.1822	0.6282	0.0361	-0.3816	0.0000	-0.0044	-0.0188	0.0413	0.0054	0.0024	-0.0182	-0.0311	0.0080	0.0020	0.0231	0.0198	-0.0433	0.0038	0.0077	-0.0359	-14.6161	59.8570	-26.8129
9	1.2928	0.1869	1.8408	1.0546	-1.1902	5.7621	0.0191	-0.0395	-0.0240	0.0683	-0.0083	-0.0397	-0.2065	0.1134	-0.0108	0.0311	-0.1048	-0.0848	-0.1544	0.0057	-0.1273	-2.0740	49.2301	-9.2927

Refine TLS group

ID	Refine ID	Refine TLS ID	Selection details
1	X-RAY DIFFRACTION	1	{A|7:57}
2	X-RAY DIFFRACTION	2	{B|7:169 233:268}
3	X-RAY DIFFRACTION	3	{B|170:232}
4	X-RAY DIFFRACTION	4	{B|269:342}
5	X-RAY DIFFRACTION	5	{F|-1-39 127:171 255:281}
6	X-RAY DIFFRACTION	6	{F|40:51 111:126 172:216 238:254}
7	X-RAY DIFFRACTION	7	{F|52:110 217:237}
8	X-RAY DIFFRACTION	8	{F|282:293}
9	X-RAY DIFFRACTION	9	{F|294:391}