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- PDB-3fwc: Sac3:Sus1:Cdc31 complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3fwc
TitleSac3:Sus1:Cdc31 complex
Components
  • Cell division control protein 31
  • Nuclear mRNA export protein SAC3
  • Protein SUS1
Keywordscell cycle / transcription / gene gating / complex / Calcium / Cell division / Mitosis / mRNA transport / Nuclear pore complex / Nucleus / Phosphoprotein / Protein transport / Translocation / Transport / Acetylation / Transcription regulation
Function / homology
Function and homology information


half bridge of spindle pole body / spindle pole body duplication / actin filament-based process / DUBm complex / mitotic spindle pole body / Golgi vesicle transport / transcription export complex 2 / nuclear pore cytoplasmic filaments / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery ...half bridge of spindle pole body / spindle pole body duplication / actin filament-based process / DUBm complex / mitotic spindle pole body / Golgi vesicle transport / transcription export complex 2 / nuclear pore cytoplasmic filaments / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SLIK (SAGA-like) complex / mRNA 3'-end processing / SAGA complex / poly(A)+ mRNA export from nucleus / nuclear pore / mRNA export from nucleus / transcription-coupled nucleotide-excision repair / protein export from nucleus / enzyme activator activity / transcription elongation by RNA polymerase II / P-body / microtubule cytoskeleton organization / protein transport / nuclear envelope / mitotic cell cycle / regulation of protein localization / chromatin organization / ribosomal small subunit biogenesis / microtubule binding / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / cell division / calcium ion binding / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2880 / Nuclear mRNA export protein Sac3 / SAC3 helical domain / Leucine permease transcriptional regulator helical domain / ENY2/SUS1 / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 / SAC3/GANP/THP3, conserved domain / SAC3/GANP/THP3 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2880 / Nuclear mRNA export protein Sac3 / SAC3 helical domain / Leucine permease transcriptional regulator helical domain / ENY2/SUS1 / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 / SAC3/GANP/THP3, conserved domain / SAC3/GANP/THP3 / SAC3/GANP family / EF hand domain / Serum Albumin; Chain A, Domain 1 / Proteasome component (PCI) domain / PCI domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EF-hand / : / Recoverin; domain 1 / Helix non-globular / EF-hand domain pair / Special / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cell division control protein 31 / Nuclear mRNA export protein SAC3 / Transcription and mRNA export factor SUS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsStewart, M. / Jani, D.
CitationJournal: Mol.Cell / Year: 2009
Title: Sus1, Cdc31, and the Sac3 CID region form a conserved interaction platform that promotes nuclear pore association and mRNA export.
Authors: Jani, D. / Lutz, S. / Marshall, N.J. / Fischer, T. / Kohler, A. / Ellisdon, A.M. / Hurt, E. / Stewart, M.
History
DepositionJan 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division control protein 31
B: Nuclear mRNA export protein SAC3
C: Protein SUS1
D: Protein SUS1
E: Cell division control protein 31
F: Nuclear mRNA export protein SAC3
G: Protein SUS1
H: Protein SUS1
I: Cell division control protein 31
J: Nuclear mRNA export protein SAC3
K: Protein SUS1
L: Protein SUS1
M: Cell division control protein 31
N: Nuclear mRNA export protein SAC3
O: Protein SUS1
P: Protein SUS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,74720
Polymers204,36216
Non-polymers3844
Water2,198122
1
A: Cell division control protein 31
B: Nuclear mRNA export protein SAC3
C: Protein SUS1
D: Protein SUS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1875
Polymers51,0914
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9230 Å2
ΔGint-93 kcal/mol
Surface area23060 Å2
MethodPISA
2
E: Cell division control protein 31
F: Nuclear mRNA export protein SAC3
G: Protein SUS1
H: Protein SUS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1875
Polymers51,0914
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-100 kcal/mol
Surface area23790 Å2
MethodPISA
3
I: Cell division control protein 31
J: Nuclear mRNA export protein SAC3
K: Protein SUS1
L: Protein SUS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1875
Polymers51,0914
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-97 kcal/mol
Surface area22740 Å2
MethodPISA
4
M: Cell division control protein 31
N: Nuclear mRNA export protein SAC3
O: Protein SUS1
P: Protein SUS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1875
Polymers51,0914
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9270 Å2
ΔGint-92 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.590, 122.710, 128.710
Angle α, β, γ (deg.)90.000, 95.750, 90.000
Int Tables number4
Space group name H-MP1211
DetailsSac3:Sus1:Cdc31 complex

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Components

#1: Protein
Cell division control protein 31 / Nucleoporin CDC31 / Nuclear pore protein CDC31


Mass: 18774.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: see publication for complete details
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CDC31, DSK1, YOR257W / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06704
#2: Protein
Nuclear mRNA export protein SAC3 / Leucine permease transcriptional regulator


Mass: 10127.569 Da / Num. of mol.: 4 / Fragment: residues 723-805
Source method: isolated from a genetically manipulated source
Details: see publication for complete ddetails
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LEP1, SAC3, YD8358.13, YDR159W / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46674
#3: Protein
Protein SUS1


Mass: 11094.497 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: see publication for complete details
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SUS1, YBR111W-A / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q6WNK7
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: unbuffered 16% PEG4K, 20% glycerol, 0.2 M Am sulph. See publication for complete details, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 30, 2008
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 61904 / Num. obs: 61904 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 2.8
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 2.8 / % possible all: 99.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FWB

3fwb


Resolution: 2.7→19.924 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.12 / Isotropic thermal model: isotropic + TLS / σ(F): 1.91 / Phase error: 30.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2646 3094 5.02 %
Rwork0.2112 --
obs0.214 61667 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.847 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso mean: 99.126 Å2
Baniso -1Baniso -2Baniso -3
1--2.496 Å2-0 Å2-8.506 Å2
2---4.472 Å20 Å2
3---2.352 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13368 0 20 122 13510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613549
X-RAY DIFFRACTIONf_angle_d0.86718197
X-RAY DIFFRACTIONf_dihedral_angle_d16.475190
X-RAY DIFFRACTIONf_chiral_restr0.0492057
X-RAY DIFFRACTIONf_plane_restr0.0032342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.74210.39991260.35552693X-RAY DIFFRACTION99
2.7421-2.78690.3331310.29282627X-RAY DIFFRACTION99
2.7869-2.83490.31331300.29392677X-RAY DIFFRACTION99
2.8349-2.88630.38791470.29122622X-RAY DIFFRACTION99
2.8863-2.94160.33161240.29392720X-RAY DIFFRACTION99
2.9416-3.00150.32021180.26872644X-RAY DIFFRACTION99
3.0015-3.06650.31971570.26792664X-RAY DIFFRACTION99
3.0665-3.13760.30511500.26322633X-RAY DIFFRACTION99
3.1376-3.21570.31481460.2472643X-RAY DIFFRACTION99
3.2157-3.30230.30821420.23732655X-RAY DIFFRACTION99
3.3023-3.3990.29341430.22162649X-RAY DIFFRACTION99
3.399-3.50810.27081140.21472722X-RAY DIFFRACTION99
3.5081-3.63280.28121510.21662608X-RAY DIFFRACTION99
3.6328-3.77730.26291530.19852667X-RAY DIFFRACTION99
3.7773-3.9480.2511450.18662679X-RAY DIFFRACTION99
3.948-4.15430.21721480.17672650X-RAY DIFFRACTION99
4.1543-4.4120.20651410.15612666X-RAY DIFFRACTION99
4.412-4.74840.20491370.15732684X-RAY DIFFRACTION99
4.7484-5.21840.24821530.17052670X-RAY DIFFRACTION99
5.2184-5.95580.27021400.21792688X-RAY DIFFRACTION99
5.9558-7.43820.27441480.22732681X-RAY DIFFRACTION99
7.4382-19.92470.21331500.16842631X-RAY DIFFRACTION96
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)
11.20612.241-0.14895.0842-0.5614-0.26631.09630.2453-0.84691.4903-0.36460.3435-0.0145-0.0794-0.69890.7985-0.0073-0.48790.49750.02520.873921.33193.8061-3.6854
21.39960.2229-2.42071.192.112-1.604-0.0537-0.463-0.1484-0.29060.30140.00831.22670.8428-0.14530.8361-0.0749-0.20350.369-0.03760.150430.7574.275611.7191
3-0.09510.1348-1.76910.29192.39225.6842-0.03910.0365-0.0046-0.15750.4056-0.07420.20910.0786-0.26840.6810.047-0.28930.3477-0.10670.271837.91574.45164.9424
43.3904-1.17380.94050.57410.88644.7993-0.2363-0.4988-1.51880.18020.23370.2501-0.48720.7067-0.22320.4638-0.0739-0.24170.5760.35560.859715.5291-11.266411.8242
55.3696-1.5949-3.9037-2.41883.98715.5018-1.0957-0.2973-1.591-0.1953-0.56330.5553-0.12860.33731.36631.0579-0.0061-0.11040.95420.29671.5630.8628-6.198316.4058
64.49450.66573.57835.7931-0.26661.7406-0.31380.1327-1.99470.7918-0.1620.3521-0.45610.44770.54030.7890.1439-0.67260.7133-0.54722.11717.6404-13.15116.6492
70.09421.0321-0.2906-4.67487.62040.15550.19850.04-0.5340.20270.17832.04740.41170.0582-0.34070.85660.3926-0.0640.56640.15061.72899.20110.316471.8251
81.78682.50381.4132.06311.11081.29960.5770.08270.25180.0682-0.6579-0.30281.43440.1240.0050.6660.00820.1070.3047-0.13170.573477.28388.737958.8568
95.9868-1.79363.03420.80760.63832.59550.917-0.14520.4018-0.7605-1.0016-0.04340.1728-0.169-0.01460.8729-0.0792-0.22270.7687-0.20290.712455.55936.072144.6274
108.91962.93895.94872.04721.1952-0.2514-0.1359-0.87910.1945-0.0619-0.217-0.06740.091-0.63090.46120.831-0.2069-0.11380.60960.01830.500241.932.593934.4333
110.3068-0.7004-0.77870.1724-3.67740.59380.6485-1.1210.04150.9835-0.25690.03770.37490.9121-0.3621.0364-0.119-0.25720.8995-0.2280.312827.38921.295421.7043
12-0.4294-0.3575-0.03793.5324-3.68190.84840.2963-0.2414-0.30650.52930.14270.8331-0.3619-0.1542-0.40970.9378-0.1078-0.31610.79230.15850.881510.1426-1.742310.1672
136.70794.80995.43992.00696.2011.6308-0.90241.05120.66110.56920.06861.15770.32870.98760.87940.8558-0.0338-0.1230.89680.56250.945554.173711.889632.8354
146.30054.5309-0.6495.15942.1065-4.4181-0.1021.4220.0539-0.48510.56-0.06470.4909-0.1333-0.42971.27040.0009-0.18820.60860.01540.339848.4061-2.07927.0202
157.78193.9962.6601-1.8633-4.42413.36821.1195-0.5259-0.92750.1169-1.1754-0.18570.9206-0.5122-0.09711.1024-0.5822-0.13920.5529-0.02840.577329.4446-7.375930.7297
169.09079.1251.52537.66498.01642.0197-0.236-2.76532.10940.4991-0.48941.57140.5817-0.26680.85470.54890.1538-0.07321.2697-0.35530.928923.61966.161630.9769
177.1983-1.4779-2.27041.45791.1274-5.8031-0.5407-2.178-0.1331.33790.2780.42230.48210.13060.19421.1668-0.3111-0.09260.72770.5536-0.950140.2095-6.423439.9239
18-4.6599-7.3461-2.89321.99988.03678.98161.1978-0.12340.0252-0.05950.4952-2.6865-1.863-0.6042-0.94120.84350.006-0.42410.04430.14550.128155.996-1.087836.2179
19-0.32211.6566-3.2304-2.8126-3.0385-0.50280.35070.00190.65470.34341.29080.6864-0.85620.2801-1.58050.9979-0.0048-0.12280.3795-0.27211.032992.038714.003278.8786
201.2643-1.73322.42853.6036-0.85735.2630.9101-0.2416-0.552-0.1740.0824-1.47030.367-0.1878-0.92830.3229-0.0347-0.08320.31630.1040.760386.854621.473468.3775
213.51610.0790.3655.2339-0.9681-0.27850.30650.2945-0.3004-0.4672-0.3484-1.07370.2510.2371-0.14670.62360.06450.25530.2083-0.26750.320379.26746.876249.8502
221.0691-1.85621.15799.35162.77120.8691-1.04830.09730.52751.0140.59882.8714-0.1889-0.03430.32390.8038-0.1752-0.00550.2179-0.18950.876266.3196-3.209156.6715
238.84630.9071-0.2570.88941.08252.95570.7939-0.7175-2.39280.6402-0.976-2.72070.45751.0565-0.3859-0.11430.84310.4238-0.5484-0.36640.723888.55637.747158.4797
244.9957-6.8427-0.51631.99976.94132.0458-0.8522-0.1142-0.3025-0.4677-1.6481-0.5355-0.1287-0.10692.60980.62930.1346-0.13410.42520.36331.509298.59922.143770.5786
252.3591-3.094-1.0534-1.0716-1.29664.1503-0.7457-0.43670.6397-0.1921-0.13160.04131.39540.2460.85260.64390.0760.04860.3795-0.16120.820346.428528.495622.8509
26-4.21353.41250.69792.34770.36071.6822-0.15570.56741.0161-0.14730.70040.74-0.6128-2.32060.00430.1447-0.15130.02740.4633-0.31180.552140.581534.711813.886
277.94851.1455-2.92191.5433-2.5953.78760.26811.8899-0.85640.45150.267-0.0564-0.3266-1.1389-0.52850.2830.01130.1290.7026-0.05050.278751.525338.769220.3566
288.31837.43647.84526.8292.37566.2799-0.97120.75462.0293-0.1897-1.45531.3271-0.02030.27190.9786-0.10.32840.5372-0.4427-1.4996-1.419545.02747.914439.0786
292.93070.16530.11823.64283.7926-4.36250.2784-1.1050.28352.1157-1.09880.05710.7440.51690.68581.1343-0.43940.0421.25380.28930.502647.247441.304951.724
306.1921-1.52746.42359.59292.74591.7635-0.34650.2930.37840.51360.3847-0.9808-0.1487-0.8040.01120.4311-0.2623-0.04130.54960.11650.527853.718448.508542.755
311.8559-5.82193.59525.6236-4.75068.83360.0454-0.39640.7995-1.2792-0.237-0.86190.6758-0.490.2450.92420.0472-0.00120.55360.06490.5268-40.808329.5871-10.5607
320.9461.80222.2811.36012.20895.16210.69490.76060.26190.20060.5097-0.58120.19771.03-1.18430.3776-0.12280.0280.634-0.25960.7538-19.379530.42782.0131
333.81480.95093.771-0.54860.09040.50150.3805-2.30030.2534-0.19920.2486-0.6534-0.2826-0.5461-0.59120.3756-0.34040.22191.3785-0.52821.04062.909933.451814.5082
34-2.9151.013.69374.088-1.01528.75671.1286-1.83291.1017-0.1127-1.0446-0.60830.4588-2.7829-0.00570.3539-0.25040.06011.0323-0.50530.87320.343134.550921.6208
351.96632.9272-2.85840.2429-0.68842.70930.3385-0.79931.81150.0048-0.51220.34890.1505-1.0460.07320.2016-0.15690.271.177-0.68810.879731.995935.485628.1171
369.59595.08463.65054.12656.60675.6807-0.0470.694-1.58470.61180.0324-0.26941.1615-0.00260.11120.42590.15790.00910.4447-0.0460.617149.06537.324339.2032
37-0.0736-3.38748.28472.03110.87871.68740.66143.479-1.0466-0.1289-0.078-1.8031-0.1692.5722-0.51860.5312-0.26020.141.7689-0.30531.162115.469334.69168.1861
38-3.80532.26330.37763.1808-0.33011.0917-0.00712.3222-0.72940.23311.8105-0.0473-0.1947-0.7709-1.77480.6797-0.2195-0.22891.0354-0.10931.778720.436647.26523.3302
39-0.2552-1.23891.59624.1604-2.6283.6115-0.71670.4427-0.17210.0522-0.92060.66530.0436-0.41861.55920.7452-0.34870.5581.3303-0.48180.886526.160540.789233.3765
40-1.4025-4.54192.75912.68090.53615.87171.4738-1.4242-1.9454-0.12212.426-1.09670.12661.8644-3.88860.323-0.2546-0.06091.0428-0.65881.3130.094627.278733.7968
41-5.16573.9585-5.61378.59141.30237.62392.0879-0.84380.40070.7262-3.01853.421-0.6801-2.90961.17440.4086-0.71610.52381.5703-0.88371.737414.628139.701527.9513
428.09375.9535-7.93846.73195.34845.0051-0.2524-0.60572.6347-0.79481.30022.9247-0.49351.0263-1.05230.1766-0.1894-0.21280.2160.07790.86256.785540.60259.785
435.6426-9.6049-0.81267.4892-2.0054.90810.2473-0.1169-0.7571-0.62510.64532.6579-1.07210.1812-0.96861.0523-0.13330.02180.67760.16620.9951-49.431825.6508-4.2871
440.7644-0.1744-3.89251.4536-5.15916.13110.1541-0.2723-0.2290.5953-0.01120.053-1.16110.3754-0.40510.5385-0.0347-0.18410.27220.06690.2968-39.566917.5482-6.0487
45-3.8140.47822.1942.106-0.21832.0685-0.4734-0.9960.21280.01570.2762-0.6368-0.02020.47380.30140.1740.0286-0.01190.4802-0.19570.6995-26.818320.0826-9.1316
460.7744-0.29740.54770.18690.09720.12680.01690.3146-0.1895-0.16230.5288-0.56760.03590.8296-0.70460.4629-0.32820.21690.8505-0.32120.9049-15.218336.1821-2.9191
475.3008-0.1573-0.1343-1.0039-0.31466.95920.7926-0.1111.3772-0.0806-0.2540.06110.55810.1354-0.44420.4931-0.12170.11790.3139-0.00120.684-25.749834.8776-6.4749
482.16691.4125-0.9761.53891.221-1.9838-0.5691.10820.1234-0.52631.0214-0.2289-0.6106-0.2941-0.27120.5396-0.1681-0.2780.83190.08890.2687-41.777819.4276-16.9203
494.68196.23040.73922.1612-2.01642.0249-0.1765-0.22342.01810.59-0.25810.887-0.7497-0.08070.25840.3579-0.1334-0.11360.07910.280.534153.77346.045866.6698
502.0621-0.7267-2.3221-1.03921.92342.91510.076-0.2378-0.38240.44390.4692-0.40390.55030.4098-0.47790.3597-0.0741-0.2060.2375-0.08680.385667.6334.059274.7291
514.2395-3.13331.7082-2.41623.11184.124-0.5545-0.16860.8984-0.9516-0.0921-0.2424-0.7451-0.29530.66580.399-0.12580.00090.17480.02830.320561.56492.134867.0575
524.91790.51242.50166.9178-0.67953.386-0.4330.119-0.0851.07940.157-0.8679-0.29830.36140.2040.24140.03010.07450.09120.01780.24840.9428-7.623682.0655
532.4564-5.4733-0.96182.67940.24292.9587-0.19080.16140.8762-0.00690.58350.4255-0.1216-0.6634-0.47520.31460.01560.08380.44520.05090.953228.5283-6.602979.0224
548.26792.5887-2.957.78534.45321.1152-0.43581.1015-1.15690.65340.6456-1.65090.2007-0.2223-0.31660.23460.0565-0.09640.2405-0.12140.545638.1213-13.113372.3364
554.7564-1.0876-8.68623.71382.5788-2.4884-0.31610.12762.1873-1.346-1.6411-0.12210.41263.70451.6430.2029-0.06571.10920.17051.3587123.79378.6662134.7083
564.24541.54630.84474.22711.72061.04030.32340.4847-0.15630.3997-0.1024-0.48560.8369-0.0131-0.30040.6152-0.0503-0.09310.4484-0.05480.4178106.80478.6061122.9403
572.02050.52782.04971.80131.56186.11910.5116-1.84130.92630.1843-0.55840.28141.8821-1.52250.09640.4122-0.1049-0.05930.5865-0.03280.266484.58426.1405107.5557
583.847-0.60456.61211.6594-1.72669.84840.0972-0.4633-0.2507-0.32160.1433-0.18640.8633-0.7631-0.06670.4699-0.123-0.15450.37680.0260.379570.59633.377195.4598
594.71470.87572.15282.33450.34523.43760.543-0.4902-0.1154-1.17620.31310.10321.002-0.301-0.76190.5878-0.2198-0.26260.29530.08670.354458.07172.232385.7271
607.8162-2.26821.5059-6.6994-5.71892.8284-0.3370.18661.09650.60720.23130.069-1.536-0.20030.04250.4644-0.057-0.17670.14980.04180.704341.4347-1.356174.662
612.02437.24234.8691-0.20991.97727.8864-1.22151.20091.4228-0.7686-0.53570.45991.64811.82321.92030.77650.0515-0.0970.84150.25160.700386.090111.329995.5216
627.22882.75067.37387.55456.30630.9431.25272.4384-0.4413-0.0771-0.41020.8261.59391.3861-1.06880.53140.2961-1.46110.5088-0.3045-2.127480.3345-0.729990.252
635.19112.32392.7376-8.5794.26263.82672.1029-0.2766-1.31610.4225-0.56040.12842.316-0.152-1.6941.3971-0.4959-0.4770.51330.33480.945564.8582-8.20794.056
642.03798.1833.50664.88091.50396.7528-0.0847-1.90431.44890.3630.22081.25180.743-1.1147-0.03060.6306-0.23840.04180.9886-0.06080.918352.72845.834792.1404
655.0529-1.15265.61764.5441-2.6192-3.80821.3476-3.4684-0.37533.0513-0.87440.0715-0.6812-1.0622-0.15671.1919-0.29950.05291.45940.29750.47563.7619-0.3873101.7847
664.09450.1998-2.3741.39272.19432.61381.241-0.34760.0917-0.98310.0667-0.33130.64450.0617-1.09060.76930.0992-0.37410.45720.08080.314984.7082-2.1236100.8766
67-9.83480.1593-5.27881.1393-0.1021.68281.2955-0.1042-0.06360.0249-1.58770.912-0.1364-2.09090.3130.9364-0.26-0.42611.4193-0.70511.4447120.902217.3312141.7104
680.1545-1.65620.17791.78030.69950.84640.3473-0.15730.7106-0.03990.3568-2.4538-0.10210.8392-0.57980.45740.0615-0.38820.7918-0.39321.2208117.296920.7062129.4167
691.0261-5.8717-4.40441.3889-1.843.72780.5963-0.6060.9079-0.5718-0.0358-1.11921.02230.5176-0.6630.3515-0.1615-0.26940.4465-0.8495-0.4604110.0046.2678114.0311
709.86117.63736.07878.12573.6112.40040.2351-0.7347-0.5878-0.3460.3747-0.3085-1.502-0.8817-0.5110.8878-0.1314-0.29670.3969-0.04830.176597.0745-3.8082120.023
71-0.379-3.47223.58089.32413.8269.44880.22220.6916-0.52210.53731.3359-3.00981.06231.8769-1.55460.26670.4201-0.39530.7175-0.56011.0546118.91116.8604123.4815
720.8707-1.307-4.8628-0.2728-0.85423.3715-0.8596-2.3644-1.4354-0.1732-2.1939-1.3815-0.3476-0.15083.1140.6187-0.1237-0.33821.46530.01441.5887130.196621.3403135.7455
739.0057-1.80429.7646-0.2281-2.0068.4018-1.11862.07570.44170.0372-0.5043-0.3033-1.29441.95291.3767-0.57830.1038-1.46420.6240.281-1.418688.140633.343983.4257
741.18863.3862-2.30761.3413-0.67692.90730.1026-0.1380.1003-0.0099-0.23320.05870.2392-0.2120.13810.2033-0.05760.11990.1947-0.01310.314770.01131.802584.1206
751.0909-0.4572-3.1746-2.8218-0.00772.6413-0.69070.25291.3602-0.10260.03840.3001-0.1282-0.95620.41010.1565-0.04730.06640.2458-0.03530.428970.168734.629672.2366
761.741-0.10212.15611.14390.25713.6250.47930.61610.0370.22550.0262-0.33440.23080.5624-0.24880.1136-0.03890.04730.2986-0.05010.122680.813238.72882.3287
777.20980.89531.61180.455-3.61276.66420.1454-1.0203-0.35610.60390.0341-0.0745-1.412-1.4762-0.13640.62090.1172-0.06990.6489-0.26220.328176.467942.5951109.3412
788.1175-2.65663.97246.65620.22180.8840.22891.3399-0.44610.5678-0.65220.11610.00450.27570.32220.6035-0.4139-0.38420.74960.42880.674684.389346.8186104.7518
795.41575.5977-2.70077.30870.59433.07720.1053-0.53110.9868-0.340.14331.6432-0.13290.2674-0.21410.1425-0.01360.03430.0280.07570.2881-9.097628.780252.5699
803.36650.09161.76570.6065-0.25972.1834-0.0161-0.08590.22210.1378-0.39160.47020.8719-0.08620.31220.20960.01630.16290.09320.0430.292212.291231.341365.2898
818.15827.7765-3.4855.39132.81382.48040.8916-1.95321.6679-0.5716-0.64920.8214-0.07850.3582-0.22220.29720.0135-0.15090.42560.10750.79828.767134.108174.8636
823.61670.97986.19722.26941.59850.5310.6595-1.90850.44420.2398-0.4697-0.49980.1829-0.5677-0.13440.21920.02110.09390.7772-0.19110.56145.859436.305882.7044
831.1608-0.2085-2.09421.06880.72950.17410.50390.12170.77020.5482-0.101-0.77860.20050.2344-0.2021-2.6176-0.91881.07950.61140.02840.142660.294636.791789.5444
842.35980.45170.51212.2671-0.39822.8622-0.11740.1067-0.3324-0.1581-0.2586-0.23380.5083-0.49910.59530.3422-0.02570.01650.4648-0.02870.324577.260436.5118100.7882
852.6774-5.85671.36093.6085-0.78850.87342.63211.07171.1353-0.0162-0.41340.14450.11192.04-2.36980.78910.175-0.00821.1316-0.29851.160940.258729.197268.7279
864.98411.9563-1.48842.11890.58463.5165-1.44340.15913.16040.83940.765-1.9415-0.36590.50560.2745-0.0396-0.58890.91220.50680.25091.022547.70741.645772.1139
873.15171.71115.72662.2404-1.81223.3023-0.8689-1.99992.3469-0.0513-0.08820.82560.2415-1.51381.05641.0645-0.33170.24931.5927-1.04281.741852.169446.433589.7528
880.65260.64941.82863.06870.2371.79840.4762-5.562-0.2321-0.22831.1403-0.2764-0.1599-0.5332-1.60660.7516-0.66620.35242.2433-0.40340.901753.058832.023296.541
89-2.8373-0.879-2.6681-0.97840.75511.373-1.53720.15180.16580.2958-0.53682.0643-0.1413-1.92012.06840.79940.14880.04941.5737-1.29392.199941.061846.04688.8415
906.7741-8.8785-8.51591.99841.8613.33390.1231-1.21722.4194-0.03361.8497-0.4459-0.14540.1018-1.83710.38610.05030.10840.62520.19970.866635.709442.419472.6666
911.02123.43731.19926.7693-8.95022.05141.6197-1.02490.2797-0.55990.84571.89590.7038-1.151-2.71340.5142-0.1743-0.08010.64410.19710.8951-16.686121.517457.3781
924.49380.81651.1655-2.1868-2.15652.64340.8965-0.0771-0.3331-0.1175-0.1191-0.26350.17910.0286-0.93570.4675-0.07340.06760.3474-0.10150.3631-0.976818.504353.8892
93-0.4149-2.67850.84842.55231.14921.77290.01720.1942-0.1462-0.2330.0208-0.5926-0.16920.67820.010.1762-0.07870.25760.2997-0.02410.333412.489332.164954.7639
947.74917.15170.64941.9032-0.56852.0121.2075-0.96850.55790.05060.3085-0.0472-0.41191.5992-1.80750.3059-0.19260.30390.541-0.06710.495617.379844.809468.0745
95-1.1339-0.07021.44071.30411.34154.59190.6183-0.39430.25820.3196-0.2865-0.27730.0594-1.0505-0.2809-0.65350.25650.28450.0113-0.07840.35757.333339.747465.8501
967.41795.1153-1.01934.28850.1711-6.1736-0.43640.36390.2109-1.72920.08090.26050.1185-0.23470.39540.7688-0.252-0.15730.57780.00230.1117-5.824524.672346.5184
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 13:19)
2X-RAY DIFFRACTION2(chain A and resid 20:59)
3X-RAY DIFFRACTION3(chain A and resid 60:89)
4X-RAY DIFFRACTION4(chain A and resid 90:112)
5X-RAY DIFFRACTION5(chain A and resid 113:150)
6X-RAY DIFFRACTION6(chain A and resid 151:161)
7X-RAY DIFFRACTION7(chain B and resid 722:728)
8X-RAY DIFFRACTION8(chain B and resid 729:754)
9X-RAY DIFFRACTION9(chain B and resid 755:764)
10X-RAY DIFFRACTION10(chain B and resid 765:776)
11X-RAY DIFFRACTION11(chain B and resid 777:790)
12X-RAY DIFFRACTION12(chain B and resid 791:805)
13X-RAY DIFFRACTION13(chain C and resid 6:13)
14X-RAY DIFFRACTION14(chain C and resid 14:32)
15X-RAY DIFFRACTION15(chain C and resid 33:47)
16X-RAY DIFFRACTION16(chain C and resid 48:68)
17X-RAY DIFFRACTION17(chain C and resid 69:83)
18X-RAY DIFFRACTION18(chain C and resid 84:95)
19X-RAY DIFFRACTION19(chain D and resid 3:12)
20X-RAY DIFFRACTION20(chain D and resid 13:27)
21X-RAY DIFFRACTION21(chain D and resid 28:53)
22X-RAY DIFFRACTION22(chain D and resid 54:60)
23X-RAY DIFFRACTION23(chain D and resid 61:87)
24X-RAY DIFFRACTION24(chain D and resid 88:95)
25X-RAY DIFFRACTION25(chain E and resid 13:41)
26X-RAY DIFFRACTION26(chain E and resid 42:81)
27X-RAY DIFFRACTION27(chain E and resid 82:93)
28X-RAY DIFFRACTION28(chain E and resid 94:113)
29X-RAY DIFFRACTION29(chain E and resid 114:147)
30X-RAY DIFFRACTION30(chain E and resid 148:161)
31X-RAY DIFFRACTION31(chain F and resid 722:734)
32X-RAY DIFFRACTION32(chain F and resid 735:754)
33X-RAY DIFFRACTION33(chain F and resid 755:769)
34X-RAY DIFFRACTION34(chain F and resid 770:778)
35X-RAY DIFFRACTION35(chain F and resid 779:788)
36X-RAY DIFFRACTION36(chain F and resid 789:805)
37X-RAY DIFFRACTION37(chain G and resid 6:28)
38X-RAY DIFFRACTION38(chain G and resid 29:38)
39X-RAY DIFFRACTION39(chain G and resid 39:49)
40X-RAY DIFFRACTION40(chain G and resid 50:63)
41X-RAY DIFFRACTION41(chain G and resid 64:81)
42X-RAY DIFFRACTION42(chain G and resid 82:95)
43X-RAY DIFFRACTION43(chain H and resid 3:11)
44X-RAY DIFFRACTION44(chain H and resid 12:22)
45X-RAY DIFFRACTION45(chain H and resid 23:31)
46X-RAY DIFFRACTION46(chain H and resid 32:57)
47X-RAY DIFFRACTION47(chain H and resid 58:83)
48X-RAY DIFFRACTION48(chain H and resid 84:95)
49X-RAY DIFFRACTION49(chain I and resid 13:30)
50X-RAY DIFFRACTION50(chain I and resid 31:73)
51X-RAY DIFFRACTION51(chain I and resid 74:94)
52X-RAY DIFFRACTION52(chain I and resid 95:126)
53X-RAY DIFFRACTION53(chain I and resid 127:149)
54X-RAY DIFFRACTION54(chain I and resid 150:161)
55X-RAY DIFFRACTION55(chain J and resid 722:730)
56X-RAY DIFFRACTION56(chain J and resid 731:754)
57X-RAY DIFFRACTION57(chain J and resid 755:767)
58X-RAY DIFFRACTION58(chain J and resid 768:778)
59X-RAY DIFFRACTION59(chain J and resid 779:789)
60X-RAY DIFFRACTION60(chain J and resid 790:805)
61X-RAY DIFFRACTION61(chain K and resid 6:15)
62X-RAY DIFFRACTION62(chain K and resid 16:29)
63X-RAY DIFFRACTION63(chain K and resid 30:44)
64X-RAY DIFFRACTION64(chain K and resid 45:59)
65X-RAY DIFFRACTION65(chain K and resid 60:78)
66X-RAY DIFFRACTION66(chain K and resid 79:95)
67X-RAY DIFFRACTION67(chain L and resid 6:16)
68X-RAY DIFFRACTION68(chain L and resid 17:30)
69X-RAY DIFFRACTION69(chain L and resid 31:52)
70X-RAY DIFFRACTION70(chain L and resid 53:60)
71X-RAY DIFFRACTION71(chain L and resid 61:86)
72X-RAY DIFFRACTION72(chain L and resid 87:95)
73X-RAY DIFFRACTION73(chain M and resid 13:18)
74X-RAY DIFFRACTION74(chain M and resid 19:55)
75X-RAY DIFFRACTION75(chain M and resid 56:81)
76X-RAY DIFFRACTION76(chain M and resid 82:93)
77X-RAY DIFFRACTION77(chain M and resid 94:148)
78X-RAY DIFFRACTION78(chain M and resid 149:161)
79X-RAY DIFFRACTION79(chain N and resid 722:738)
80X-RAY DIFFRACTION80(chain N and resid 739:754)
81X-RAY DIFFRACTION81(chain N and resid 755:765)
82X-RAY DIFFRACTION82(chain N and resid 766:778)
83X-RAY DIFFRACTION83(chain N and resid 779:787)
84X-RAY DIFFRACTION84(chain N and resid 788:805)
85X-RAY DIFFRACTION85(chain O and resid 6:15)
86X-RAY DIFFRACTION86(chain O and resid 16:29)
87X-RAY DIFFRACTION87(chain O and resid 30:47)
88X-RAY DIFFRACTION88(chain O and resid 48:69)
89X-RAY DIFFRACTION89(chain O and resid 70:78)
90X-RAY DIFFRACTION90(chain O and resid 79:95)
91X-RAY DIFFRACTION91(chain P and resid 3:18)
92X-RAY DIFFRACTION92(chain P and resid 19:29)
93X-RAY DIFFRACTION93(chain P and resid 30:49)
94X-RAY DIFFRACTION94(chain P and resid 50:55)
95X-RAY DIFFRACTION95(chain P and resid 56:69)
96X-RAY DIFFRACTION96(chain P and resid 70:95)

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  • 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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