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- PDB-3kik: Sgf11:Sus1 complex -

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Basic information

Entry
Database: PDB / ID: 3kik
TitleSgf11:Sus1 complex
Components
  • Protein SUS1
  • SAGA-associated factor 11
KeywordsTRANSCRIPTION / articulated hirpin fold / SAGA complex / Activator / Chromatin regulator / Metal-binding / Nucleus / Transcription regulation / Zinc / Zinc-finger / mRNA transport / Nuclear pore complex / Protein transport / Translocation / Transport
Function / homology
Function and homology information


DUBm complex / : / transcription export complex 2 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear mRNA surveillance / SLIK (SAGA-like) complex / SAGA complex / poly(A)+ mRNA export from nucleus / enzyme activator activity / mRNA export from nucleus ...DUBm complex / : / transcription export complex 2 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear mRNA surveillance / SLIK (SAGA-like) complex / SAGA complex / poly(A)+ mRNA export from nucleus / enzyme activator activity / mRNA export from nucleus / nuclear pore / transcription elongation by RNA polymerase II / P-body / regulation of protein localization / protein transport / chromatin organization / transcription coactivator activity / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Yeast SAGA-associated factor 11, N-terminal domain / SAGA-associated factor 11 N-terminal domain / ENY2/SUS1 / SAGA complex, Sgf11 subunit / Sgf11 (transcriptional regulation protein) / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 / Serum Albumin; Chain A, Domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
SAGA-associated factor 11 / Transcription and mRNA export factor SUS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStewart, M. / Ellisdon, A.M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural basis for the interaction between yeast Spt-Ada-Gcn5 acetyltransferase (SAGA) complex components Sgf11 and Sus1
Authors: Ellisdon, A.M. / Jani, D. / Kohler, A. / Hurt, E. / Stewart, M.
History
DepositionNov 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein SUS1
E: SAGA-associated factor 11
B: Protein SUS1
F: SAGA-associated factor 11
C: Protein SUS1
G: SAGA-associated factor 11
D: Protein SUS1
H: SAGA-associated factor 11


Theoretical massNumber of molelcules
Total (without water)56,6768
Polymers56,6768
Non-polymers00
Water4,630257
1
A: Protein SUS1
E: SAGA-associated factor 11


Theoretical massNumber of molelcules
Total (without water)14,1692
Polymers14,1692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-25 kcal/mol
Surface area7590 Å2
MethodPISA
2
B: Protein SUS1
F: SAGA-associated factor 11


Theoretical massNumber of molelcules
Total (without water)14,1692
Polymers14,1692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-26 kcal/mol
Surface area7470 Å2
MethodPISA
3
C: Protein SUS1
G: SAGA-associated factor 11


Theoretical massNumber of molelcules
Total (without water)14,1692
Polymers14,1692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-26 kcal/mol
Surface area7380 Å2
MethodPISA
4
D: Protein SUS1
H: SAGA-associated factor 11


Theoretical massNumber of molelcules
Total (without water)14,1692
Polymers14,1692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-25 kcal/mol
Surface area7490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.153, 75.153, 197.373
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsSAGA complex

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Components

#1: Protein
Protein SUS1


Mass: 11094.497 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: see publication for details
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SUS1, YBR111W-A / Plasmid: pNMTK / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) / References: UniProt: Q6WNK7
#2: Protein/peptide
SAGA-associated factor 11 / 11 kDa SAGA-associated factor


Mass: 3074.420 Da / Num. of mol.: 4 / Fragment: Sus1 binding region of Sgf11
Source method: isolated from a genetically manipulated source
Details: see publication for details
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SGF11, YPL047W / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q03067
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3.2 M Na formate. See publication for details, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54059 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 4, 2009 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54059 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 36176 / Num. obs: 36176 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 26.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.4 / Num. unique all: 5136 / % possible all: 95.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 2FWB residues 21-90 of chain C
Resolution: 2.1→19.86 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.39 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 1991 5.52 %Random but accounting for merohedral symmetry using PHENIX
Rwork0.195 ---
obs0.197 36040 98.37 %-
all-36167 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.407 Å2 / ksol: 0.413 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 0 0 257 4071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027694
X-RAY DIFFRACTIONf_angle_d0.51713957
X-RAY DIFFRACTIONf_dihedral_angle_d13.9812027
X-RAY DIFFRACTIONf_chiral_restr0.038651
X-RAY DIFFRACTIONf_plane_restr0.0011193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.14040.2051080.24141838X-RAY DIFFRACTION98
2.1404-2.1840.26661080.24611832X-RAY DIFFRACTION98
2.184-2.23140.25671070.24051835X-RAY DIFFRACTION98
2.2314-2.28330.25551040.2481870X-RAY DIFFRACTION98
2.2833-2.34030.21471110.24711869X-RAY DIFFRACTION98
2.3403-2.40350.26661090.23041835X-RAY DIFFRACTION98
2.4035-2.4740.29621100.23861860X-RAY DIFFRACTION98
2.474-2.55370.23771080.24121893X-RAY DIFFRACTION98
2.5537-2.64480.27711120.22881888X-RAY DIFFRACTION98
2.6448-2.75050.2671110.23441925X-RAY DIFFRACTION98
2.7505-2.87530.34641120.22791919X-RAY DIFFRACTION98
2.8753-3.02640.26051030.21351930X-RAY DIFFRACTION98
3.0264-3.21520.2761130.2031914X-RAY DIFFRACTION98
3.2152-3.46230.20211110.1981925X-RAY DIFFRACTION98
3.4623-3.80850.21771160.16771925X-RAY DIFFRACTION98
3.8085-4.35450.15041180.13821926X-RAY DIFFRACTION98
4.3545-5.46720.18461150.15571924X-RAY DIFFRACTION98
5.4672-19.86090.28291140.20951942X-RAY DIFFRACTION98
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL112)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)
1refined0.15490.6259-0.22470.24570.09810.4284-0.8659-0.652-0.54340.2474-0.3646-0.9958-0.7186-0.19060.00160.72690.0007-0.14570.53360.11840.920225.707366.6696-3.5298
20.14760.0468-0.28680.1359-0.0440.2088-0.4582-0.7491-0.7969-0.4949-0.47180.08670.68050.1544-0.00110.5728-0.10280.09240.4693-0.15261.4494
30.1201-0.0302-0.23230.15290.02520.1947-1.0813-0.7708-1.1049-0.13340.5409-0.731-0.0377-0.26460.00090.49330.05990.01970.357-0.08280.8036
40.03560.0896-0.17550.1258-0.10230.06870.4356-0.34-0.57240.5641-0.05790.0974-0.769-0.13280.0010.7871-0.0694-0.15720.7331-0.04750.4582
50.38990.1932-0.36530.3608-0.30870.3081-0.3701-0.5278-0.54450.79180.27650.27170.0559-1.12-0.00020.47210.15160.06650.6981-0.14340.3941
60.12650.01970.04680.1066-0.11050.09460.36571.5679-0.91990.2611-0.9434-0.0069-1.1985-1.70890.00270.72760.43580.02491.0726-0.22170.5537
70.16230.15530.27860.8465-0.00960.2088-0.0527-0.18990.38780.56230.0755-0.1241-0.6504-0.73390.00020.47160.1309-0.08460.5095-0.13780.4068
80.31350.0645-0.03930.05580.01790.2998-0.7393-1.33961.07911.21020.0075-0.0355-1.7552-0.12260.00320.61150.1745-0.21310.6971-0.11150.5804
90.53250.4291-0.41770.21410.29390.4546-0.2683-1.1335-0.3742-0.02950.1829-0.0478-0.87850.55430.00050.64190.0006-0.17560.46610.06110.504
100.3752-0.0334-0.0680.28860.41520.062-0.6133-1.0448-0.54710.4171-0.0514-1.86750.34250.7281-0.00290.4553-0.11-0.13720.44340.29960.7452
110.1289-0.13190.0640.1037-0.2076-0.02060.50380.3854-0.02750.3695-1.2389-0.50590.60170.97230.00040.6542-0.04920.08290.69160.08071.0761
120.16080.0426-0.16760.08860.01510.1345-0.8127-0.6198-0.31870.2752-0.0915-1.00881.8409-0.8935-0.00040.7159-0.09470.09890.7911-0.10130.8344
130.2474-0.04330.20240.13950.10540.17670.2-0.4620.51051.00180.49790.09750.2591.0219-0.00040.41880.0717-0.02770.5833-0.10920.4593
140.53010.25770.23250.20110.80290.0828-0.05340.32430.6075-0.12950.0518-0.13460.04210.32940.00010.44280.02740.00730.38060.01580.3718
150.2488-0.0110.17750.2411-0.04510.1547-0.99550.76670.538-0.98820.6813-0.38850.7514-0.40950.0010.5798-0.0860.02610.5093-0.03610.4452
160.50370.3350.14120.47910.02650.17630.4246-0.0684-0.0395-0.94330.38620.55740.7048-0.1474-0.00060.7281-0.1113-0.08790.4469-0.04710.4305
170.743-0.0790.105-0.07730.13470.24860.5321-0.1221-0.3752-0.4637-0.14190.4750.91610.289400.55840.0782-0.02080.404-0.10010.5047
180.73740.4711-0.26090.47410.2070.499-0.0379-0.0279-0.2287-0.64930.4691-0.12150.66130.6039-0.0010.65040.16070.15550.6426-0.01960.4827
190.64310.24740.090.06930.61090.3197-0.14550.28720.3409-0.1526-0.08230.45890.74971.1443-0.00010.54360.09820.03830.67860.04140.4984
20-0.0759-0.07390.08020.31540.00480.09781.00350.51031.8777-1.2434-1.32061.0008-1.87130.97120.00040.6194-0.06580.23380.8939-0.01981.3542
21-0.041-0.03120.0482-0.053-0.0387-0.0290.46051.05310.5541-0.05730.0457-0.4691-1.541-0.89010.00050.97750.4883-0.2491.0198-0.36671.2162
220.1529-0.0205-0.03340.2856-0.05260.13510.1518-0.19731.3974-0.915-0.1878-0.0134-0.9707-0.00280.00010.81990.0923-0.05430.49010.00310.6881
230.4022-0.10170.14580.448-0.79990.07810.4863-0.17150.461-0.14080.0220.3080.1273-0.05610.00090.29820.03270.08450.29420.02530.3322
240.1794-0.01250.25420.1951-0.2460.1940.1647-0.2554-0.00340.99480.1722-0.2811-0.44330.7101-0.00050.4637-0.0114-0.04460.41370.03590.4394
250.15840.9190.53260.1833-0.49070.49050.3816-0.4332-0.11180.3382-0.312-0.38980.9888-0.3588-0.00020.5248-0.12580.02170.49020.04850.2031
26-0.0106-0.002-0.10860.04940.08880.09181.2698-1.67950.1462-0.60730.07230.01090.2689-0.224-0.00080.9601-0.37530.24931.09610.26950.901
270.077-0.4052-0.15130.4403-0.15520.22970.3114-0.43930.30420.177-0.2412-0.040.8498-1.9757-0.00170.3556-0.1075-0.02960.76410.02690.3561
280.45830.1983-0.0120.1253-0.15860.37950.1647-0.64150.35680.57920.11680.8511-0.5335-0.9112-0.00180.4301-0.00650.0970.6471-0.04430.4104
290.1045-0.3949-0.3860.6234-0.42510.69610.63820.02680.10171.3875-0.88990.18470.0399-0.26710.00030.4409-0.01580.08710.6497-0.06810.4569
300.0502-0.040.05440.1453-0.1226-0.0736-0.2244-0.24610.2544-0.0482-0.0206-1.1619-0.00610.9150.00060.51640.051-0.04510.70990.04380.8713
310.13350.11590.05520.5644-0.21490.2411-0.63020.13120.022-0.42910.1963-0.0636-0.933-1.0868-0.00020.59610.087-0.05880.4126-0.1821.106
320.03960.0001-0.23590.1821-0.01950.1196-0.6811-0.39150.2139-0.743-0.74660.60280.705-0.1072-0.00350.71050.00380.04930.4560.00420.8979
330.13090.0456-0.23580.2004-0.09380.2215-0.4081-0.1742-0.66-0.8489-0.05340.677-0.37510.16470.00050.50090.0461-0.01540.38490.01870.7199
340.07190.0807-0.11390.08760.05090.2663-0.20120.9585-1.0794-0.92730.06820.56271.059-0.4918-00.6066-0.15610.00650.4679-0.07090.5509
350.71810.46320.03830.41270.22940.4949-0.352-0.0661-0.2721-0.980.62850.01950.32330.3697-0.00070.6021-0.2928-0.0570.81190.0610.3767
360.08520.00620.05880.0754-0.0248-0.1321-0.9575-1.67170.86591.67031.71110.3958-0.7156-0.0826-0.00291.4122-0.55060.14981.5866-0.08770.6068
370.3909-0.2434-0.13950.11570.1240.1941-0.51850.29430.49030.06860.27020.0283-0.69590.2297-0.00060.4412-0.1536-0.12170.38760.16340.4979
380.3323-0.07420.03420.1340.3910.1069-0.88830.40060.595-0.57760.42470.4702-0.98420.45950.00260.6001-0.1354-0.12580.47620.06370.431
390.7565-0.6514-0.0470.2522-0.0920.6122-0.40931.3133-0.5085-0.58130.35490.37240.11020.17910.00030.54440.0354-0.13120.5789-0.11820.4716
400.23340.325-0.35820.3817-0.19190.1214-0.41621.1234-1.90780.2986-0.3849-0.0528-0.4037-1.2898-0.00130.55110.0358-0.01650.638-0.16850.6127
410.14040.2562-0.3315-0.02220.23320.153-0.4586-1.4241-0.9603-0.12930.0705-0.09-0.26010.3690.00060.51320.0202-0.11850.3813-0.02780.4398
420.0869-0.31590.0780.02270.11110.3446-0.0441-0.02640.29650.16990.0905-0.67480.1601-0.09870.00040.42190.0622-0.08120.3486-0.07550.3974
430.29180.41670.16010.2112-0.09220.39820.25360.4067-0.96160.5975-0.09980.4029-0.1697-0.73970.00040.54280.07060.02660.5686-0.03180.3984
440.13810.08350.1072-0.0710.05690.2539-0.83980.2383-0.8895-0.64670.2408-0.12881.15720.23030.0010.45370.03990.07780.5056-0.04970.7565
450.09850.12480.02690.0605-0.1219-0.06340.0244-1.1531-0.84190.53840.1356-1.3259-0.42220.4740.00110.48720.0368-0.01530.60090.07690.5252
460.09350.15770.41830.2537-0.52890.542-0.0279-0.10470.08620.0234-0.2673-0.4878-0.2378-0.5835-0.00020.43530.0438-0.08640.4593-0.10360.4513
470.0783-0.031-0.10570.009-0.0604-0.0340.799-0.74710.52541.0524-1.32391.0261-1.3563-1.38510.00080.82560.13760.18150.6806-0.24070.72
480.0449-0.10460.18030.21470.08530.07970.33370.29980.3714-0.3968-0.3431.11430.0766-0.05230.00110.52790.1539-0.040.60540.10260.4559
49-0.07850.51260.60140.3646-0.0640.62560.4146-0.2388-0.03010.4028-0.2163-0.71650.30920.00540.00050.45130.04770.07440.540.11960.4303
500.302-0.0756-0.13010.2405-0.13450.68150.36290.1230.0464-0.3382-0.15230.126-0.59780.2237-0.00030.4643-0.0028-0.12960.2475-0.00950.4192
510.08630.2403-0.2041-0.14890.06160.0199-0.17720.4444-0.00810.0963-0.08030.0180.13150.4088-0.00030.329-0.0438-0.04560.40370.1210.478
520.2679-0.14220.09830.06290.00720.2532-0.19340.44560.0902-0.41860.39911.05430.11070.9566-0.00240.5118-0.01420.00160.4890.07480.3903
Refinement TLS groupSelection details: chain H and resid 26:32)

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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