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- PDB-6q8i: Nterminal domain of human SMU1 in complex with human REDmid -

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Basic information

Entry
Database: PDB / ID: 6q8i
TitleNterminal domain of human SMU1 in complex with human REDmid
Components
  • (Protein Red) x 2
  • WD40 repeat-containing protein SMU1
KeywordsSPLICING / Splicing factor / minimal RED-SMU1 complex
Function / homology
Function and homology information


U2-type precatalytic spliceosome / protein localization to kinetochore / regulation of alternative mRNA splicing, via spliceosome / mitotic spindle assembly checkpoint / RNA splicing / mRNA splicing, via spliceosome / spindle pole / chromosome / mitotic cell cycle / nuclear speck ...U2-type precatalytic spliceosome / protein localization to kinetochore / regulation of alternative mRNA splicing, via spliceosome / mitotic spindle assembly checkpoint / RNA splicing / mRNA splicing, via spliceosome / spindle pole / chromosome / mitotic cell cycle / nuclear speck / viral process / nucleoplasm / identical protein binding / nucleus / cytoplasm
LisH-like dimerisation domain / RED-like, N-terminal / C-terminal to LisH (CTLH) motif profile. / LIS1 homology (LisH) motif profile. / Trp-Asp (WD) repeats circular profile. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats signature. / RED-like protein N-terminal region / RED-like protein C-terminal region / WD domain, G-beta repeat ...LisH-like dimerisation domain / RED-like, N-terminal / C-terminal to LisH (CTLH) motif profile. / LIS1 homology (LisH) motif profile. / Trp-Asp (WD) repeats circular profile. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats signature. / RED-like protein N-terminal region / RED-like protein C-terminal region / WD domain, G-beta repeat / Protein Red-like / WD40-repeat-containing domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / WD40-repeat-containing domain / WD40/YVTN repeat-like-containing domain superfamily / Protein RED, C-terminal / CTLH, C-terminal LisH motif / LIS1 homology motif / WD40 repeat
Protein Red / WD40 repeat-containing protein SMU1
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsTengo, L. / Le Corre, L. / Fournier, G. / Ashraf, U. / Busca, P. / Rameix-Welti, M.-A. / Gravier-Pelletier, C. / Ruigrok, R.W.H. / Jacob, Y. / Vidalain, P.-O. / Pietrancosta, N. / Naffakh, N. / McCarthy, A.A. / Crepin, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Destabilization of the human RED-SMU1 splicing complex as a basis for host-directed antiinfluenza strategy.
Authors: Ashraf, U. / Tengo, L. / Le Corre, L. / Fournier, G. / Busca, P. / McCarthy, A.A. / Rameix-Welti, M.A. / Gravier-Pelletier, C. / Ruigrok, R.W.H. / Jacob, Y. / Vidalain, P.O. / Pietrancosta, N. / Crepin, T. / Naffakh, N.
Validation Report
SummaryFull reportAbout validation report
History
DepositionDec 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WD40 repeat-containing protein SMU1
B: WD40 repeat-containing protein SMU1
C: Protein Red
D: Protein Red
E: WD40 repeat-containing protein SMU1
F: WD40 repeat-containing protein SMU1
G: Protein Red
H: Protein Red
I: WD40 repeat-containing protein SMU1
J: WD40 repeat-containing protein SMU1
K: Protein Red
L: Protein Red
M: WD40 repeat-containing protein SMU1
N: WD40 repeat-containing protein SMU1
O: Protein Red
P: Protein Red


Theoretical massNumber of molelcules
Total (without water)986,93816
Polymers986,93816
Non-polymers00
Water0
1
A: WD40 repeat-containing protein SMU1
B: WD40 repeat-containing protein SMU1
C: Protein Red
D: Protein Red


Theoretical massNumber of molelcules
Total (without water)246,7304
Polymers246,7304
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9980 Å2
ΔGint-84 kcal/mol
Surface area22800 Å2
MethodPISA
2
E: WD40 repeat-containing protein SMU1
F: WD40 repeat-containing protein SMU1
G: Protein Red
H: Protein Red


Theoretical massNumber of molelcules
Total (without water)246,7304
Polymers246,7304
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
ΔGint-79 kcal/mol
Surface area22890 Å2
MethodPISA
3
I: WD40 repeat-containing protein SMU1
J: WD40 repeat-containing protein SMU1
K: Protein Red
L: Protein Red


Theoretical massNumber of molelcules
Total (without water)246,7474
Polymers246,7474
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9980 Å2
ΔGint-85 kcal/mol
Surface area22910 Å2
MethodPISA
4
M: WD40 repeat-containing protein SMU1
N: WD40 repeat-containing protein SMU1
O: Protein Red
P: Protein Red


Theoretical massNumber of molelcules
Total (without water)246,7304
Polymers246,7304
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9280 Å2
ΔGint-75 kcal/mol
Surface area23400 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)127.983, 68.163, 145.296
Angle α, β, γ (deg.)90.00, 109.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
WD40 repeat-containing protein SMU1 / Smu-1 suppressor of mec-8 and unc-52 protein homolog


Mass: 57673.797 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMU1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2TAY7
#2: Protein/peptide
Protein Red / Cytokine IK / IK factor / Protein RER


Mass: 65691.445 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IK, RED, RER / Production host: Escherichia coli (E. coli) / References: UniProt: Q13123
#3: Protein/peptide Protein Red / Cytokine IK / IK factor / Protein RER


Mass: 65707.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IK, RED, RER / Production host: Escherichia coli (E. coli) / References: UniProt: Q13123

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Hepes pH 7.0-7.5, 8-10 % PEG 8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.17→49 Å / Num. obs: 39441 / % possible obs: 94.3 % / Redundancy: 2.4 % / Biso Wilson estimate: 74.61 Å2 / Rrim(I) all: 0.144 / Net I/σ(I): 6.9
Reflection shellResolution: 3.17→3.25 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.14 / Num. unique obs: 2828 / Rrim(I) all: 1.146 / % possible all: 97.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q8F
Resolution: 3.17→49 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.858 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.502
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1940 4.92 %RANDOM
Rwork0.256 ---
Obs0.257 39441 90.8 %-
Displacement parametersBiso mean: 132.34 Å2
Baniso -1Baniso -2Baniso -3
1--22.1794 Å20 Å25.0498 Å2
2--14.7258 Å20 Å2
3---7.4536 Å2
Refine analyzeLuzzati coordinate error obs: 0.7 Å
Refinement stepCycle: 1 / Resolution: 3.17→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13701 0 0 0 13701
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumberRestraint functionWeight
t_bond_d0.00813902HARMONIC2
t_angle_deg0.9818866HARMONIC2
t_dihedral_angle_d4826SINUSOIDAL2
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes349HARMONIC2
t_gen_planes1982HARMONIC5
t_it13902HARMONIC20
t_nbd
t_omega_torsion1.71
t_other_torsion20.43
t_improper_torsion
t_chiral_improper_torsion1899SEMIHARMONIC5
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact15260SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 141 4.81 %
Rwork0.252 2789 -
All0.253 2930 -
Obs--92.75 %
Refinement TLS params.

Method: refined / Refinement-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.00262.35150.15289.17430.72381.42330.03640.1514-0.0681-0.0358-0.02630.49910.0625-0.3555-0.01010.87950.07-0.0530.2245-0.04490.0621-53.3897-4.973-54.2743
21.80790.97260.42852.36020.73813.137-0.1189-0.5588-0.30870.79120.2196-1.43210.20450.3378-0.10071.5320.1461-0.28170.37140.00950.6967-27.80068.2694-33.146
31.05413.1103-1.406111.00622.48150.2769-0.24010.22870.1893-0.11840.34280.48740.0098-0.0585-0.10271.15960.03110.08680.24810.07630.1826-40.647-0.1759-62.7712
47.2-4.2911.97541.6277-2.66727.0718-0.0318-0.6785-0.38380.13860.1347-0.2528-0.0122-0.1405-0.10290.83180.03310.09760.4369-0.06710.5208-45.636714.4685-33.8011
52.3998-2.23360.49398.6932-0.64470.3505-0.057-0.1587-0.00320.05710.1593-0.6157-0.13830.204-0.10220.8892-0.0580.00570.2754-0.02180.0735-53.629-29.1461-16.6707
63.0249-0.83381.34622.59662.64313.8195-0.41070.9509-0.0004-0.5888-0.13691.5323-0.1785-0.96360.54761.8268-0.4545-0.06821.00420.05820.7414-82.2232-15.0343-31.233
7-0.2866-1.2220.16088.0575-5.19651.3981-0.10470.0810.08330.47470.2497-0.0458-0.2302-0.0072-0.1451.297-0.16850.0440.4153-0.02060.3555-58.4407-18.9204-20.0286
86.36261.50092.41721.28362.72039.0152-0.08430.7011-0.4581-0.64780.15640.1918-0.26020.5981-0.07211.15340.04510.04670.30530.01410.4395-72.8727-14.6854-18.1579
91.25410.77030.87268.54661.88731.64770.0613-0.30790.17850.172-0.2270.6448-0.2387-0.41180.16570.773-0.0202-0.35850.56210.00690.6314-19.1291-13.83445.6285
103.7362-1.15014.66110.6052-0.61127.8758-0.33110.39160.1844-0.69590.1427-0.4049-0.89270.51930.18831.6383-0.2649-0.270.23760.07240.5662-25.3588-26.6005-27.6612
114.7538-0.6925-0.65095.51514.4992-0.7850.04490.2842-0.08070.2126-0.1152-0.2884-0.0585-0.20240.07031.15940.0266-0.47090.41890.06030.5503-5.5602-17.3243-2.8841
124.53780.751-0.56920.13741.14884.9847-0.1167-0.81320.21710.1947-0.1361-0.1598-0.7377-0.02020.25291.2847-0.1925-0.32590.3795-0.04360.4765-33.5482-32.0243-11.7456
136.5695-2.66022.48791.251-2.39583.8270.02170.55880.6786-0.07-0.0726-0.3829-0.01590.71320.05092.2578-0.1607-0.45111.3278-0.00941.3147-84.6557-38.6046-72.8165
144.71011.1624.42423.96031.15055.27480.2409-0.9464-0.24410.22520.3477-0.6876-0.0313-0.8466-0.58861.91590.1446-0.30870.9540.0711.4199-82.2035-51.3159-38.9829
153.4543-1.45874.53585.18870.26174.49920.2690.42380.3291-0.6186-0.5414-1.8232-0.384-0.21830.27241.79560.0298-0.30070.86-0.22331.6611-98.6319-41.0608-66.5164
16-0.72-1.53353.46065.92087.46525.43890.79680.4480.2887-1.5272-1.78040.3311-0.2255-1.08190.98362.3201-0.03-0.10451.3510.03190.9621-73.0982-57.291-53.7784
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection details
11{ A|3 - A|189 }
22{ B|3 - B|188 }
33{ C|207 - C|257 }
44{ D|211 - D|257 }
55{ E|3 - E|188 }
66{ F|3 - F|188 }
77{ G|208 - G|257 }
88{ H|211 - H|257 }
99{ I|3 - I|188 }
1010{ J|2 - J|188 }
1111{ K|206 - K|257 }
1212{ L|211 - L|257 }
1313{ M|3 - M|188 }
1414{ N|3 - N|188 }
1515{ O|207 - O|257 }
1616{ P|211 - P|257 }

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