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- PDB-3muu: Crystal structure of the Sindbis virus E2-E1 heterodimer at low pH -

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Entry
Database: PDB / ID: 3muu
TitleCrystal structure of the Sindbis virus E2-E1 heterodimer at low pH
DescriptorStructural polyprotein (E.C.3.4.21.-)
KeywordsVIRAL PROTEIN / Beta barrels / Ig-like folds
Specimen sourceSindbis virus / virus / SINV / シンドビスウイルス
MethodX-ray diffraction (3.29 Å resolution / MAD)
AuthorsLi, L. / Jose, J. / Xiang, Y. / Kuhn, R.J. / Rossmann, M.G.
CitationNature, 2010, 468, 705-708

Nature, 2010, 468, 705-708 Yorodumi Papers
Structural changes of envelope proteins during alphavirus fusion.
Li, L. / Jose, J. / Xiang, Y. / Kuhn, R.J. / Rossmann, M.G.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 3, 2010 / Release: Nov 24, 2010
RevisionDateData content typeGroupCategoryProviderType
1.0Nov 24, 2010Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance
1.2Jul 26, 2017Structure modelRefinement description / Source and taxonomyentity_src_gen / software

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Assembly

Deposited unit
A: Structural polyprotein
B: Structural polyprotein
C: Structural polyprotein
D: Structural polyprotein
E: Structural polyprotein
F: Structural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)505,69956
Polyers495,7066
Non-polymers9,99350
Water0
#1
A: Structural polyprotein
B: Structural polyprotein
C: Structural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,85028
Polyers247,8533
Non-polymers4,99725
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
#2
D: Structural polyprotein
E: Structural polyprotein
F: Structural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,85028
Polyers247,8533
Non-polymers4,99725
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)67.482, 158.430, 160.676
Angle α, β, γ (deg.)60.42, 89.80, 89.65
Int Tables number1
Space group name H-MP 1

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Components

#1: Polypeptide(L)
Structural polyprotein / p130 / Capsid protein / Coat protein / C / p62 / E3/E2 / E3 protein / Spike glycoprotein E3 / E2 envelope glycoprotein / Spike glycoprotein E2 / 6K protein / E1 envelope glycoprotein / Spike glycoprotein E1


Mass: 82617.719 Da / Num. of mol.: 6
Source: (gene. exp.) Sindbis virus / virus / シンドビスウイルス
References: UniProt: P03316, EC: 3.4.21.-

Cellular component

Molecular function

Biological process

#2: Chemical...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 24 / Formula: C8H15NO6
#3: Chemical
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 12 / Formula: C6H12O6
#4: Chemical
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 14 / Formula: C6H12O6

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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: 3.01 / Density percent sol: 59.16
Crystal growTemp: 293 K / pH: 5.6
Details: PEG8000 10%, Sodium/Potassium Tartrate 325 mM, Sodium/Potassium Phosphate 100 mM pH5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: APS BEAMLINE 23-ID-B / Synchrotron site: APS / Beamline: 23-ID-B / Wavelength: 0.97934,0.97951,0.94934
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Collection date: Oct 31, 2009
RadiationMonochromator: SI(111) / Diffraction protocol: MAD / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelength
IDWavelengthRelative weight
10.979341.0
20.979511.0
30.949341.0
ReflectionD resolution high: 3.3 Å / D resolution low: 7 Å / Number obs: 162989 / Observed criterion sigma I: -3 / Rmerge I obs: 0.128 / Rsym value: 0.128 / NetI over sigmaI: 12.5 / Redundancy: 3.8 / Percent possible obs: 97.3
Reflection shellRmerge I obs: 0.658 / Highest resolution: 3.3 Å / Lowest resolution: 3.36 Å / MeanI over sigI obs: 1.8 / Rsym value: 0.658 / Redundancy: 3.4 / Percent possible all: 82.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefineMethod to determine structure: MAD / Overall SU ML: 0.35 / Sigma F: 1.96 / Overall phase error: 28.28 / Stereochemistry target values: ML_SAD
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL / Solvent model param bsol: 69.49 / Solvent model param ksol: 0.27
Displacement parametersAniso B11: 40.8597 Å2 / Aniso B12: -2.2902 Å2 / Aniso B13: -0.2614 Å2 / Aniso B22: -15.5516 Å2 / Aniso B23: 5.1022 Å2 / Aniso B33: -25.3081 Å2
Least-squares processR factor R free: 0.252 / R factor R work: 0.239 / R factor obs: 0.24 / Highest resolution: 3.29 Å / Lowest resolution: 60.72 Å / Number reflection R free: 8227 / Number reflection all: 176472 / Number reflection obs: 162989 / Percent reflection R free: 5.05 / Percent reflection obs: 92.4
Refine hist #LASTHighest resolution: 3.29 Å / Lowest resolution: 60.72 Å
Number of atoms included #LASTProtein: 28537 / Nucleic acid: 0 / Ligand: 622 / Solvent: 0 / Total: 29159
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00729988
X-RAY DIFFRACTIONf_angle_d1.23540957
X-RAY DIFFRACTIONf_dihedral_angle_d23.49211016
X-RAY DIFFRACTIONf_chiral_restr0.0804770
X-RAY DIFFRACTIONf_plane_restr0.0055142
Refine LS restraints ncs

Refine ID: X-RAY DIFFRACTION / Type: POSITIONAL

Dom IDAuth asym IDEns IDNumberRms dev position
1A121490.029
2B121490.029
3C121450.031
4D121490.020
5E121490.026
6F121450.038
1A218740.024
2B218740.024
3C218740.022
4D218660.015
5E218740.018
6F218480.016
1A36400.014
2B36400.014
3C36400.029
4D36400.016
5E36400.011
6F36400.009
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
3.28520.39610.37183.4026452887753.00
3.40260.34930.33153.53887581468487.00
3.53880.34140.32583.69998561611096.00
3.69990.29020.28583.89498461644398.00
3.89490.25780.25414.13899571641598.00
4.13890.25210.21704.45849561648798.00
4.45840.18490.18024.90688701630198.00
4.90680.19100.18625.61648661657298.00
5.61640.21250.19957.07448541645499.00
7.07440.25250.236960.73358121641997.00
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
1-0.5355-1.2157-1.76481.82251.50171.34320.03730.24780.18960.59620.0808-0.09070.39570.6696-0.00030.4703-0.09180.03770.1075-0.01270.369437.212141.972155.1748
2-0.19820.02150.44940.43450.31621.70580.02410.1176-0.0687-0.0877-0.0950-0.2583-0.49730.2398-0.00280.43450.09590.03210.3672-0.06590.333437.6389103.374961.5421
3-1.00052.0048-0.07731.3541-1.15650.74050.2475-0.31380.2521-0.5089-0.0351-0.50240.32110.21190.08150.30570.0361-0.03990.25320.09820.221937.276378.05864.5403
4-0.73040.4552-0.99421.2799-0.59360.5764-0.0366-0.08690.1884-0.77290.20630.21760.5383-0.67600.01320.43520.08130.03490.18350.02000.377041.8644120.889772.4170
50.15940.00791.04190.30840.00332.35070.0127-0.1551-0.03990.0053-0.06540.1939-0.7014-0.2020-0.00030.4125-0.10670.01010.32790.04560.289841.9898182.469065.9988
6-0.2063-1.1877-0.37761.98321.32391.30040.05060.0992-0.03710.48970.09020.28630.3816-0.13340.02040.33320.0276-0.08310.2983-0.05740.268742.0484157.3294122.8845
70.3700-0.33120.19380.2750-0.16760.09070.63510.08440.2719-0.3175-0.5850-0.6143-0.04310.1854-0.00012.2290-0.09030.60051.56250.00451.323859.836319.212614.0082
80.09220.21230.00530.4920-0.06830.14790.61220.80210.10860.2824-0.1337-1.63830.50220.2660-0.00111.74320.5474-0.07771.26740.11851.126160.355378.8213101.5324
90.07790.0693-0.13130.0288-0.10020.16870.4631-0.49490.0076-0.18830.0362-0.4417-0.53460.7884-0.00032.1544-0.1732-0.36911.2606-0.15021.439160.6725124.10346.1697
100.19560.17390.17270.19550.08470.21260.6410-0.48830.83530.5542-0.55500.50440.1858-0.54800.00022.49860.27460.82001.4864-0.13441.548118.735198.5507113.5256
110.2372-0.3316-0.16370.44930.21810.11120.5479-0.8538-0.68010.2148-0.51531.07190.11100.3209-0.00032.1065-0.4795-0.06221.51640.02401.538519.2533158.106425.7818
120.3717-0.1248-0.23710.14080.02620.17830.04471.1804-0.0126-0.4269-0.02010.4045-1.1349-0.5393-0.00032.52850.4903-0.50771.52580.10101.425419.1337204.3335122.0135
131.0269-0.77670.25121.9943-1.18941.91020.09620.0407-0.57210.20700.12590.5115-0.3686-0.6036-0.00040.4248-0.14920.22140.71670.03500.73786.433763.646753.4278
141.14570.3150-0.06651.94810.58451.44940.1133-0.17230.1534-0.3048-0.22070.5776-0.1731-0.47870.00000.47830.28080.01470.6476-0.08180.70966.584191.201643.3107
150.4480-0.3804-0.17001.63500.46152.0147-0.06130.25410.1732-0.1588-0.06250.42900.3451-0.50830.00020.5095-0.0896-0.17010.8021-0.01450.54976.439968.727424.2769
160.6656-0.57330.11632.73281.20151.42710.0817-0.1126-0.1148-0.37840.1388-0.6808-0.00870.5883-0.00010.59910.17360.17860.7927-0.04780.807173.0032142.537874.2229
170.9666-0.9404-0.03692.6200-1.18971.51170.00210.35140.30770.2307-0.1901-0.7137-0.37080.7211-0.00010.3765-0.28050.06820.65210.04620.662872.8465170.370384.3349
180.6620-0.1823-0.79760.9632-0.40321.37590.0382-0.39520.2712-0.0919-0.1706-0.24900.34160.48270.00000.54740.1392-0.21870.75890.07050.533172.8297147.8197103.2329
190.2834-0.15730.14040.0562-0.07790.0695-0.13970.6521-0.63260.2347-0.60470.6914-0.1014-0.15520.00050.5076-0.14650.23600.8148-0.12980.986317.022048.534944.0058
200.86370.52250.56080.31910.31360.3194-0.4302-0.8666-0.1595-0.21920.0139-0.3419-0.3735-1.1398-0.00060.58210.37400.13811.0429-0.10710.649516.758791.345960.6746
210.65380.4491-0.54420.5790-0.33810.4363-0.24310.85100.9484-0.44270.92200.97430.43260.5587-0.00390.0486-0.0366-0.39640.61690.17500.680416.877084.327315.9440
220.55400.39710.01750.26470.0086-0.00080.0169-0.2647-0.6711-0.6428-0.7180-0.6097-0.2559-0.16360.00250.25660.23840.22420.69490.13790.978261.9418127.744084.4041
230.3488-0.29150.34830.2392-0.28230.3468-0.12330.62790.09390.14140.01580.4178-0.27560.7991-0.00170.5032-0.31870.11760.9824-0.00780.645062.5722169.864366.5112
240.1187-0.0470-0.02080.0503-0.01120.00120.2816-0.35210.46000.41100.4475-0.60910.2721-0.14140.00110.31440.1319-0.24740.6284-0.13810.872061.6751165.3545110.4699
251.0726-0.66471.19131.2134-0.23421.61860.36430.1520-0.2374-0.2774-0.2204-0.0838-0.17510.1030-0.00050.3204-0.06190.14140.53270.14850.451444.225051.681827.5484
261.20911.2975-0.14331.4067-0.48721.45530.3538-0.50290.0512-0.2607-0.1638-0.05520.30330.0837-0.00010.48320.1597-0.01330.3769-0.04670.670444.035074.787566.3885
270.4845-0.5998-0.22541.2163-0.18190.51570.16800.29920.10090.3851-0.2211-0.06720.1948-0.03310.00020.3015-0.1070-0.12070.5024-0.08730.283544.214296.638026.9387
280.98860.38390.45451.4157-0.80451.85720.2246-0.1758-0.2502-0.1534-0.06790.1023-0.40410.0450-0.00020.14000.11710.19010.4514-0.16530.310635.2129131.132699.8783
291.1095-1.06030.03401.15350.50391.50970.12000.2712-0.04120.5596-0.10630.03930.1658-0.07800.00050.2883-0.1986-0.00720.21970.01660.562135.3494154.048961.2387
300.97520.6263-0.86851.3425-0.11340.92250.1694-0.23620.2358-0.1413-0.0518-0.11160.2664-0.04190.00020.24010.0497-0.15280.55000.12810.298035.2718175.8809100.6286
Refine TLS group
IDRefine IDRefine TLS IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 358:653 OR RESSEQ 761:765)
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 358:653 OR RESSEQ 761:765)
3X-RAY DIFFRACTION3CHAIN C AND (RESSEQ 358:653 OR RESSEQ 761:765)
4X-RAY DIFFRACTION4CHAIN D AND (RESSEQ 358:653 OR RESSEQ 761:765)
5X-RAY DIFFRACTION5CHAIN E AND (RESSEQ 358:653 OR RESSEQ 761:765)
6X-RAY DIFFRACTION6CHAIN F AND (RESSEQ 358:653 OR RESSEQ 761:765)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 654:740)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 654:740)
9X-RAY DIFFRACTION9CHAIN C AND (RESSEQ 654:740)
10X-RAY DIFFRACTION10CHAIN D AND (RESSEQ 654:740)
11X-RAY DIFFRACTION11CHAIN E AND (RESSEQ 654:740)
12X-RAY DIFFRACTION12CHAIN F AND (RESSEQ 654:740)
13X-RAY DIFFRACTION13CHAIN A AND (RESSEQ 4:143)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 4:143)
15X-RAY DIFFRACTION15CHAIN C AND (RESSEQ 4:143)
16X-RAY DIFFRACTION16CHAIN D AND (RESSEQ 4:143)
17X-RAY DIFFRACTION17CHAIN E AND (RESSEQ 4:143)
18X-RAY DIFFRACTION18CHAIN F AND (RESSEQ 4:143)
19X-RAY DIFFRACTION19CHAIN A AND (RESSEQ 144:268)
20X-RAY DIFFRACTION20CHAIN B AND (RESSEQ 144:268)
21X-RAY DIFFRACTION21CHAIN C AND (RESSEQ 144:268)
22X-RAY DIFFRACTION22CHAIN D AND (RESSEQ 144:268)
23X-RAY DIFFRACTION23CHAIN E AND (RESSEQ 144:268)
24X-RAY DIFFRACTION24CHAIN F AND (RESSEQ 144:268)
25X-RAY DIFFRACTION25CHAIN A AND (RESSEQ 269:343 OR RESSEQ 751:754)
26X-RAY DIFFRACTION26CHAIN B AND (RESSEQ 269:343 OR RESSEQ 751:754)
27X-RAY DIFFRACTION27CHAIN C AND (RESSEQ 269:342 OR RESSEQ 751:754)
28X-RAY DIFFRACTION28CHAIN D AND (RESSEQ 269:344 OR RESSEQ 751:754)
29X-RAY DIFFRACTION29CHAIN E AND (RESSEQ 269:342 OR RESSEQ 751:754)
30X-RAY DIFFRACTION30CHAIN F AND (RESSEQ 269:344 OR RESSEQ 751:754)

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