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- PDB-6hc2: Crystal structure of NuMA/LGN hetero-hexamers -

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Basic information

Entry
Database: PDB / ID: 6hc2
TitleCrystal structure of NuMA/LGN hetero-hexamers
Components
  • G-protein-signaling modulator 2
  • Nuclear mitotic apparatus protein 1
KeywordsCELL CYCLE / Cell division Asymmetric cell division Spindle orientation Force generator
Function / homology
Function and homology information


anastral spindle assembly / positive regulation of protein localization to spindle pole body / positive regulation of mitotic spindle elongation / cytoplasmic microtubule bundle / positive regulation of chromosome separation / Mitotic Prophase / positive regulation of chromosome segregation / microtubule minus-end / cortical microtubule / microtubule bundle ...anastral spindle assembly / positive regulation of protein localization to spindle pole body / positive regulation of mitotic spindle elongation / cytoplasmic microtubule bundle / positive regulation of chromosome separation / Mitotic Prophase / positive regulation of chromosome segregation / microtubule minus-end / cortical microtubule / microtubule bundle / lateral cell cortex / cell cortex region / maintenance of centrosome location / mitotic spindle astral microtubule / positive regulation of intracellular transport / regulation of metaphase plate congression / mitotic spindle midzone / positive regulation of hair follicle development / astral microtubule organization / positive regulation of spindle assembly / microtubule minus-end binding / microtubule plus-end / positive regulation of BMP signaling pathway / positive regulation of keratinocyte differentiation / spindle pole centrosome / microtubule bundle formation / microtubule plus-end binding / GDP-dissociation inhibitor activity / dynein complex binding / nucleus organization / mitotic spindle pole / establishment of mitotic spindle orientation / lateral plasma membrane / G-protein alpha-subunit binding / positive regulation of protein localization to cell cortex / regulation of mitotic spindle organization / positive regulation of microtubule polymerization / Recruitment of NuMA to mitotic centrosomes / tubulin binding / phosphatidylinositol binding / mitotic spindle organization / meiotic cell cycle / spindle microtubule / mitotic spindle / nuclear matrix / spindle pole / spindle / : / disordered domain specific binding / chromosome / cell cortex / G alpha (i) signalling events / microtubule binding / G protein-coupled receptor signaling pathway / protein domain specific binding / cell division / nucleotide binding / centrosome / neuronal cell body / dendrite / protein-containing complex binding / structural molecule activity / protein-containing complex / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / : / NuMA N-terminal hook domain / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat ...: / : / NuMA N-terminal hook domain / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
G-protein-signaling modulator 2 / Nuclear mitotic apparatus protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.31 Å
AuthorsPasqualato, S. / Culurgioni, S. / Foadi, J. / Alfieri, A. / Mapelli, M.
Funding support Italy, 2items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchIG 18629 Italy
RF-2013-02357254 Italy
CitationJournal: Nat Commun / Year: 2019
Title: Hexameric NuMA:LGN structures promote multivalent interactions required for planar epithelial divisions.
Authors: Pirovano, L. / Culurgioni, S. / Carminati, M. / Alfieri, A. / Monzani, S. / Cecatiello, V. / Gaddoni, C. / Rizzelli, F. / Foadi, J. / Pasqualato, S. / Mapelli, M.
History
DepositionAug 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: G-protein-signaling modulator 2
B: Nuclear mitotic apparatus protein 1
C: G-protein-signaling modulator 2
D: Nuclear mitotic apparatus protein 1
E: G-protein-signaling modulator 2
F: Nuclear mitotic apparatus protein 1
G: G-protein-signaling modulator 2
H: Nuclear mitotic apparatus protein 1
I: G-protein-signaling modulator 2
J: Nuclear mitotic apparatus protein 1
K: G-protein-signaling modulator 2
L: Nuclear mitotic apparatus protein 1
M: G-protein-signaling modulator 2
N: Nuclear mitotic apparatus protein 1
O: G-protein-signaling modulator 2
P: Nuclear mitotic apparatus protein 1
Q: G-protein-signaling modulator 2
R: Nuclear mitotic apparatus protein 1
S: G-protein-signaling modulator 2
T: Nuclear mitotic apparatus protein 1
U: G-protein-signaling modulator 2
V: Nuclear mitotic apparatus protein 1
W: G-protein-signaling modulator 2
X: Nuclear mitotic apparatus protein 1


Theoretical massNumber of molelcules
Total (without water)582,03624
Polymers582,03624
Non-polymers00
Water00
1
A: G-protein-signaling modulator 2
B: Nuclear mitotic apparatus protein 1
C: G-protein-signaling modulator 2
D: Nuclear mitotic apparatus protein 1
E: G-protein-signaling modulator 2
F: Nuclear mitotic apparatus protein 1


Theoretical massNumber of molelcules
Total (without water)145,5096
Polymers145,5096
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15580 Å2
ΔGint-96 kcal/mol
Surface area58280 Å2
MethodPISA
2
G: G-protein-signaling modulator 2
H: Nuclear mitotic apparatus protein 1
I: G-protein-signaling modulator 2
J: Nuclear mitotic apparatus protein 1
K: G-protein-signaling modulator 2
L: Nuclear mitotic apparatus protein 1


Theoretical massNumber of molelcules
Total (without water)145,5096
Polymers145,5096
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15490 Å2
ΔGint-93 kcal/mol
Surface area58120 Å2
MethodPISA
3
M: G-protein-signaling modulator 2
N: Nuclear mitotic apparatus protein 1
O: G-protein-signaling modulator 2
P: Nuclear mitotic apparatus protein 1
Q: G-protein-signaling modulator 2
R: Nuclear mitotic apparatus protein 1


Theoretical massNumber of molelcules
Total (without water)145,5096
Polymers145,5096
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15540 Å2
ΔGint-92 kcal/mol
Surface area57750 Å2
MethodPISA
4
S: G-protein-signaling modulator 2
T: Nuclear mitotic apparatus protein 1
U: G-protein-signaling modulator 2
V: Nuclear mitotic apparatus protein 1
W: G-protein-signaling modulator 2
X: Nuclear mitotic apparatus protein 1


Theoretical massNumber of molelcules
Total (without water)145,5096
Polymers145,5096
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15760 Å2
ΔGint-83 kcal/mol
Surface area57910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.940, 153.940, 732.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
G-protein-signaling modulator 2 / Mosaic protein LGN


Mass: 40755.629 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPSM2, LGN / Production host: Escherichia coli (E. coli) / References: UniProt: P81274
#2: Protein
Nuclear mitotic apparatus protein 1 / Nuclear matrix protein-22 / NMP-22 / Nuclear mitotic apparatus protein / NuMA protein / SP-H antigen


Mass: 7747.409 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUMA1, NMP22, NUMA / Production host: Escherichia coli (E. coli) / References: UniProt: Q14980

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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: 3.73 Å3/Da / Density % sol: 67.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% PEG3350, 0.05M Bis-Tris propane and 0.1M Na-formate or 0.1M Na-acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9698 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9698 Å / Relative weight: 1
ReflectionResolution: 4.29→243.48 Å / Num. obs: 61354 / % possible obs: 99.9 % / Redundancy: 98.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.343 / Net I/σ(I): 19.1
Reflection shellResolution: 4.29→4.4 Å / Redundancy: 88.7 % / Rmerge(I) obs: 7.028 / Mean I/σ(I) obs: 2.1 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 3SF4 and 3RO2

3sf4

3ro2


Resolution: 4.31→150.653 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2341 3058 5.02 %
Rwork0.1816 --
obs0.1842 60924 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.31→150.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37562 0 0 0 37562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00538247
X-RAY DIFFRACTIONf_angle_d1.00351693
X-RAY DIFFRACTIONf_dihedral_angle_d6.95822609
X-RAY DIFFRACTIONf_chiral_restr0.0655587
X-RAY DIFFRACTIONf_plane_restr0.0066878
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)
1-0.1227-0.0502-0.5447-0.0042-0.3594-0.0875-0.05840.04250.10430.39440.01070.0115-0.0949-0.070501.9563-0.0006-0.05982.261-0.40332.148828.3038114.3531-97.7578
20.0335-0.00170.040.1767-0.00090.11760.01710.0733-0.59590.04370.0292-0.5088-0.0608-0.1091-02.665-0.277-0.15112.3157-0.27942.673914.011135.0002-106.2694
30.1489-0.1376-0.18950.123-0.32670.1816-0.4211-0.6486-0.1519-0.61210.51220.40840.12620.341701.9277-0.03920.10912.08620.02051.9235-7.5022120.8516-118.9431
40.0157-0.01680.050.0311-0.06780.1576-0.1191-0.0294-0.097-0.0345-0.07330.0203-0.0140.05380.00022.9916-0.2504-0.42593.6472-0.23112.8405-3.4915123.5824-74.3029
50.01340.00570.0057-0.00150.00050.00510.20430.1802-0.02650.02150.06950.10010.00680.142901.9873-0.41720.22042.1885-0.14212.3129-4.3387119.2778-84.1014
6-0.00630.0046-0.01120.0287-0.0050.0653-0.3842-0.2031-0.0037-0.1131-0.05920.1938-0.03490.046703.14750.36130.39142.84180.3322.8043-9.6452135.2083-95.3145
70.00120.00340.00510.00050.00420.00290.0644-0.0886-0.06730.0202-0.0629-0.03930.1354-0.009702.865-0.7363-0.28772.946-0.07043.3674-8.9494130.7638-108.3116
80.113-0.0373-0.00540.00480.0172-0.00090.09170.0009-0.0767-0.05580.28670.01520.09920.04060.00012.7554-0.54140.10172.4881-0.3092.7463.1147126.5026-109.3393
90.0346-0.01450.01030.01580.0048-0.001-0.1113-0.0812-0.03450.0085-0.16460.082-0.09410.0786-02.99490.1377-0.41982.7248-0.32273.178918.6617123.9274-107.0874
100.00350-0.00050.0045-0.00170.0018-0.06760.0359-0.0547-0.0356-0.09960.00730.06680.041502.2268-0.1971-0.31312.22620.10592.436430.9907116.5293-107.694
110.00820.00040.00050.01240.00490.0050.16810.01590.0303-0.18350.28-0.1216-0.0806-0.0763-0.00012.26660.34080.02531.76680.03542.364541.6521114.2446-104.0242
120.0880.24280.04820.6110.86230.55020.4357-0.02980.08340.2263-0.04470.2829-0.24880.415202.0366-0.0850.01241.9375-0.05371.8076-13.4599103.075-82.7787
130.32530.8136-0.6360.436-0.2783-0.4837-2.2377-0.09060.81412.45130.3663-0.5085-2.9880.43430-11.2625-0.82654.21620.57220.5093-1.1501-19.353469.8617-81.3076
140.0527-0.005-0.06210.03040.02760.0042-0.1963-0.0677-0.3811-0.0364-0.34250.42550.17240.214102.4749-0.01530.40332.7556-0.4833.56230.178972.2458-68.1458
15-0.0142-0.02080.01670.00480.0063-0.00690.147-0.1577-0.25940.18550.21020.01950.30750.3855-02.1614-0.01280.13982.34070.21542.3785-20.233887.3546-81.0359
160.00610.0115-0.00280.00390.0012-0.0095-0.103-0.09480.06090.0105-0.180.0276-0.10520.229401.43380.1929-0.07942.0559-0.0913.1742-23.4915108.7861-88.7461
170.19-0.2138-0.42410.32840.2327-0.3881-0.0541-0.8586-0.04950.05010.0632-0.066-0.1483-0.023401.3111-0.2404-0.1291.9583-0.01571.436525.612672.489-75.1123
180.71650.14870.86620.39830.2311-0.09580.5644-0.0257-0.3352-2.1065-0.84620.2297-0.8893-0.0021-0-0.7317-0.4143-0.09180.48520.24870.289946.160775.1174-101.9642
190.03320.0190.03520.02290.02110.0553-0.04690.1194-0.01470.04790.18410.13370.0631-0.1573-0.00042.4564-0.1557-0.00822.5994-0.04932.204337.0173105.263-85.0772
20-0.0265-0.0082-0.00720.00420.025-0.001-0.016-0.03230.25720.01050.20250.0027-0.2515-0.0702-0.00013.25910.2218-0.61173.065-0.37322.288343.9072101.2519-90.5829
210.01790.0037-0.00830.0015-0.00260.0038-0.04910.06540.08020.038-0.0088-0.00670.0138-0.03260.00022.30290.52010.27183.59720.05922.433645.418581.2011-98.8981
220.0114-0.0018-0.00940.0229-0.00840.01980.0428-0.084-0.071-0.10720.02070.1002-0.0612-0.11102.4252-0.0158-0.6662.59240.42.809140.075671.9685-87.9786
230.01510.001-0.00570.01680.00040.01140.1541-0.08290.1521-0.05990.0744-0.1172-0.11520.0569-02.33740.09970.35652.58780.22832.329627.955865.3351-80.5715
240.0080.0366-0.02440.7396-0.51190.35760.0386-0.0417-0.05080.0180.0834-0.01520.03270.0685-0.00222.43030.01130.18962.8760.54012.942921.240861.0565-80.2125
250.00260.002-0.00050.0018-0.0020.00280.0052-0.0838-0.1250.12060.0375-0.00650.0716-0.0057-01.79850.2223-0.05392.65520.57442.256217.654558.7266-72.9029
260.01030.01340.01830.05740.02340.0371-0.0914-0.08360.02530.05150.0004-0.01910.0128-0.0581-0.00022.56920.1428-0.40772.72580.00282.48813.331452.0959-69.2613
27-0.0651-0.19160.12490.0938-0.0029-0.3542-0.40180.4037-0.6043-0.4710.2579-0.39040.1669-0.5933-01.54270.08320.25781.93490.21122.3062-37.828639.2485-71.2092
280.1159-0.0165-0.0388-0.0506-0.25580.07550.376-0.04460.038-0.0318-0.10870.6473-0.38030.181801.59210.14150.15341.60350.1632.154-48.932660.4629-73.9407
290.01440.12780.06820.01340.28460.10440.42710.1246-0.3456-0.43990.32270.15010.09910.6476-01.81910.1378-0.01621.5443-0.0432.017-67.475965.6936-79.9508
30-0.0908-0.13310.03810.033-0.2310.07520.08830.80510.3282-0.23550.130.3326-0.1529-0.260701.48320.0042-0.14162.16870.38722.1778-67.226962.6528-90.8759
31-0.0065-0.011-0.11540.1135-0.1850.2863-0.07860.1270.66480.2252-0.0949-0.41540.4201-0.171301.5024-0.0180.05912.05620.37162.1977-83.684545.2535-85.066
320.0186-0.049-0.05530.06260.00750.05660.04010.45040.02250.1595-0.4842-0.03750.3785-0.786300.3726-0.25830.16320.62160.29370.7888-95.860144.6007-66.9142
330.0047-0.00340.00250.0068-0.0079-0.0046-0.0931-0.0054-0.0143-0.2921-0.0101-0.0842-0.1060.026702.5719-0.0573-0.0681.98890.32852.9671-79.660272.7996-62.7178
340.01580.03970.00920.0245-0.04180.0175-0.13790.23590.3665-0.39090.1024-0.3585-0.0457-0.2224-02.22660.0684-0.18023.03030.24442.1435-81.206657.9074-79.5945
350.0066-0.02070.0225-0.0192-0.0109-0.0010.067-0.235-0.00510.1133-0.1427-0.0263-0.17940.5225-02.0904-0.2971-0.20842.40040.08841.4767-54.157949.836-82.3575
360.00750.00920.0108-0.00520.00060.01020.0683-0.01120.1937-0.02760.13130.1435-0.2327-0.151802.2096-0.3906-0.75692.4935-0.151.6309-37.524547.2508-81.9057
37-0.00150.06160.087-0.1980.1374-0.09930.12170.77360.63780.6180.1519-0.01840.1013-0.377102.21620.1754-0.54692.11390.27482.1417-92.625857.4854-60.1512
380.03290.01940.02810.02680.08880.0534-0.0467-0.0166-0.16620.1863-0.3608-0.28730.13850.388502.4398-0.3239-0.26332.05130.22962.193-81.355567.1685-49.0645
390.0359-0.0908-0.07670.00580.02550.05880.07460.28810.0002-0.4032-0.39130.1694-0.0801-0.053802.9806-0.2352-0.73262.0526-0.09782.5482-80.967977.3289-39.8848
400.0406-0.0869-0.01650.02560.09630.0356-0.5805-0.33120.1175-0.62080.2016-0.09780.0950.354602.7738-0.0849-0.28262.2432-0.14922.2761-77.023670.6899-24.9578
410.0039-0.0284-0.0315-0.08910.05730.07750.1837-0.3128-0.743-0.327-0.4753-0.3673-0.7223-0.1086-02.5111-0.1286-0.37742.17420.03762.7759-84.937673.3928-22.2567
420.07590.1564-0.23070.1868-0.0874-0.0376-0.3264-0.21540.003-0.177-0.0971-0.0048-0.35580.0497-01.91810.138-0.38131.83780.01072.1906-87.537852.9087-13.2593
430.1097-0.0709-0.101-0.04740.11240.0602-1.31630.37020.0325-0.31820.7414-0.28880.34850.432701.2448-0.0483-0.36611.28480.17691.5587-67.905837.951-12.0391
440.018-0.042-0.0804-0.01460.0836-0.09040.0561-0.1658-0.3922-0.38090.06940.73610.01830.2945-01.35840.2281-0.08371.65510.07711.6331-61.784363.8126-18.6022
45-0.0126-0.0552-0.0017-0.00030.00380.00940.22210.05270.566-0.19280.5040.0811-0.00060.123902.87070.11830.00662.06720.18341.7712-88.771762.3189-34.4446
46-0.0011-0.00450.00090.0023-0.0031-0.0003-0.1235-0.095-0.0075-0.0361-0.1476-0.04530.03120.0211-02.48850.1038-0.22042.70050.00312.9512-97.347868.429-52.4146
47-0.17660.2154-0.26790.060.0019-0.0546-0.76330.0770.22130.53950.6174-0.28970.7842-0.2682-01.7591-0.2111-0.13221.93120.07461.5986-54.548747.3004-15.1525
480.2632-0.2108-0.29830.20460.0612-0.05350.0527-0.2763-0.32870.10340.0658-0.5046-0.17050.146901.5436-0.0824-0.08091.75390.10451.3305-39.574159.3107-29.9504
490.08260.05150.11720.2523-0.2115-0.02511.36451.525-0.4378-2.7669-0.06291.07641.10520.8308-0-0.3946-0.59060.2980.56510.81240.9237-25.746953.5683-43.4687
500.4478-0.27970.18310.20920.07260.52070.2727-0.24510.09270.08060.0273-0.1195-0.1748-0.038301.6917-0.03720.00361.65480.04711.7318-22.142435.2003-43.2681
510.05610.12880.07230.1123-0.10740.12020.88491.0588-0.2264-0.22780.7888-0.00530.60980.7208-00.5117-0.08690.12970.06810.7025-0.0219-35.514824.8347-66.4208
520.001-0.02280.00180.00670.0366-0.0069-0.36490.40820.2601-0.0714-0.3448-0.6080.388-0.0499-02.02560.31960.00722.022-0.15261.2432-33.24760.8918-63.1495
53-0.0353-0.0035-0.05290.018-0.0804-0.0382-0.3656-0.6161-0.6784-0.2292-0.18120.8365-0.2832-0.535201.776-0.0686-0.13221.7652-0.04262.0523-26.02343.4098-47.3565
540.0085-0.0118-0.0242-0.06450.0833-0.03440.3051-0.78130.07860.25140.3483-0.07810.0899-0.26840-0.18810.0806-0.59530.41220.08780.2923-39.660751.7504-13.9335
550.40690.4534-0.0258-0.3324-0.08180.0147-0.1645-0.11680.47450.07310.012-0.072-0.0179-0.0449-01.4090.1259-0.10331.163-0.00091.6483-30.431881.9652-4.8257
560.5802-0.14270.61811.0011-0.43190.13490.2231-0.26090.01480.4278-0.02810.20340.1107-0.225400.33930.06750.04520.57530.00070.3877-46.101171.287723.7056
570.06680.08120.04260.0217-0.0064-0.01380.26490.1734-0.5012-0.0391-0.23280.3938-0.0525-0.7547-03.0488-0.37150.04782.5450.01232.0435-51.761497.042616.2064
58-0.00770.0093-0.01470.02530.0031-0.00650.33680.0473-0.0154-0.5936-0.3454-0.17120.46230.0042-01.8169-0.0222-0.44832.01640.15791.9877-41.429374.40389.6342
590.0103-0.01840.0327-0.0213-0.00160.014-0.04770.5120.2704-0.3108-0.35620.1815-0.08070.0551-02.098-0.35560.03661.6727-0.04221.7975-21.464271.2289-9.8388
60-0.1436-0.0584-0.11420.3580.0980.2172-0.22030.10910.2455-0.00180.3530.321-0.0821-0.437802.0390.1611-0.09582.21660.30762.3637-39.6723118.49426.2056
61-0.0279-0.0745-0.37410.5576-0.15080.065-1.1236-0.36220.3042-1.261.35310.4558-1.24762.01560-0.90351.4777-0.8823-0.67820.62260.2717-10.1989129.879441.3642
620.00530.00120.00680.012-0.00130.0103-0.11360.1522-0.1452-0.08360.0321-0.0242-0.1771-0.062901.86420.48040.07932.8137-0.27962.3031-16.1067134.12654.1747
630.00630.00260.00320.0450.00840.00420.1896-0.12420.0256-0.03990.1169-0.0201-0.01880.026700.70450.2147-0.4682.52541.20581.3776-10.3811132.18649.1077
640.00910.00430.00330.0072-0.0046-0-0.0514-0.0763-0.18120.0851-0.0526-0.15230.00180.05810.00012.7126-0.38230.25662.5850.17122.3493-9.429142.214221.2496
650.0005-0.0066-0.00180.0168-0.0028-0.03010.0584-0.1324-0.22970.49160.53210.20680.0908-0.229502.69930.3785-0.72752.2814-0.46643.0032-18.0611129.973234.2306
660.02620.01440.00040.0185-0.00160.0002-0.14940.11470.06610.0299-0.229-0.0798-0.088-0.07402.48970.272-0.04512.39360.0372.0154-36.2302119.034834.7926
670.0066-0.0084-0.0090.01080.0151-0.00370.00940.17450.0138-0.07560.055-0.14860.13870.293702.1450.15690.11382.114-0.47222.3467-50.3329108.815735.0464
680.7523-0.30770.56590.3485-0.17160.367-0.1440.31430.1830.1680.0957-0.1063-0.0896-0.1342-01.4567-0.0624-0.18931.4513-0.02561.49460.1181120.48621.1655
691.52570.66720.4329-0.1219-0.84040.33070.0636-0.13920.0747-0.1313-0.3162-0.0326-0.00960.2073-00.4297-0.0666-0.07560.07220.05450.584714.058392.2017-8.5187
70-0.0061-0.00730.00390.0081-0.0328-0.0015-0.0926-0.05460.33850.03-0.05390.4049-0.042-0.026601.7909-0.3183-0.36931.35380.02972.5033-14.966391.181-19.5734
71-0.03880.0341-0.10190.0269-0.0510.01670.0194-0.72760.5458-0.0142-0.05260.19030.05420.272101.75980.06020.05771.7547-0.0131.669710.1956103.5256-6.6872
720.04890.007-0.00870.00110.02040.02010.00640.1234-0.6087-0.15770.0674-0.1604-0.2246-0.2115-00.3620.00770.30410.6855-0.56280.21518.76131.1646.6584
73-0.1169-0.00070.0181-0.0460.1748-0.12350.07080.29630.174-0.002-0.4293-0.1567-0.09630.4608-01.73090.10210.0361.68510.31591.738139.2093-31.5425-24.5985
74-0.0149-0.0175-0.09620.03040.1208-0.0563-0.07580.1730.6039-0.2730.2101-0.51310.51220.337201.686-0.21050.34971.4383-0.14771.607733.2183-19.9402-25.5978
75-0.1050.1153-0.33210.04840.26120.11220.4207-0.6387-0.2615-0.1522-0.1011-0.882-0.031-0.1438-01.6306-0.0364-0.02761.2437-0.04351.454322.0665-10.3175-15.4422
76-0.00080.01740.20220.0740.07850.02110.3557-0.73630.2687-0.0854-0.38340.2710.3374-0.219-01.84120.02110.09031.4124-0.01271.356523.89974.2603-2.2339
770.4737-0.37570.22360.1833-0.07690.2262-0.06780.44140.13030.1567-0.20270.14820.33210.0994-01.5196-0.03830.03331.7779-0.1381.749544.90189.47862.261
780.1145-0.32410.1030.0966-0.0280.11321.1497-0.36240.63520.3913-0.34470.2866-1.29311.84980-0.70450.42060.00750.5996-0.19630.659552.519427.7926-14.9763
79-0.00360.0048-0.01460.0042-0.012-0.00770.0936-0.258-0.07450.1070.1654-0.18880.0751-0.5133-01.92320.04670.39821.8158-0.06951.947917.053823.9387-18.0316
800.0070.0576-0.01020.0472-0.0933-0.0402-0.180.05730.1361-0.6107-0.18550.0189-0.3028-0.219602.4346-0.11540.17541.77130.15021.709626.305829.1586-7.7588
810.0030.00740.0010.01860.01430.0078-0.0709-0.1375-0.0053-0.01190.0361-0.00430.01140.1121-02.1751-0.5157-0.0152.6478-0.32122.597241.438417.2573-5.6301
820.00650.0254-0.00440.0065-0.00870.01220.2274-0.05180.8448-0.14260.0611-0.1247-0.0686-0.22302.6894-0.41520.24222.0679-0.18261.901735.5598-4.0007-6.5507
830.0016-0.00510.0047-0.00150.00260.0093-0.21350.0370.0230.1592-0.1283-0.1837-0.17630.123801.6636-0.1518-0.10682.13010.16421.254732.7486-20.7703-12.9685
84-0.00360.0057-0.0136-0.0014-0.0071-0.00140.05340.0906-0.078-0.10330.0925-0.0695-0.24520.082901.4562-0.0381-0.11451.71890.17121.316128.3487-30.4586-10.1153
850.2004-0.17940.0461-0.0999-0.04720.01250.4006-0.42250.04720.42420.1235-0.2623-0.23240.809701.9511-0.13830.16072.2378-0.37941.790837.824232.8693-20.9914
86-0.03710.2788-0.0385-0.1254-0.0240.1334-0.1050.28880.57750.0446-0.12080.16220.13620.248401.6312-0.07810.00582.7045-0.04721.859115.927231.9728-42.4427
87-0.2961-0.34750.2420.1688-0.1790.19260.35990.6572-0.6756-0.54180.14290.3889-0.6261-0.2289-0-0.86240.2357-1.83980.79291.631-4.840834.051431.4927-68.7814
88-0.0003-0.00540.00410.0075-0.01180.0142-0.02860.00730.03590.04960.0580.0133-0.00510.06740.00012.98790.47510.31312.5585-0.42332.71795.31399.3521-62.5519
890.0041-0.00210.00780.0065-0.00420.0165-0.05410.02950.1146-0.1710.04890.00630.00660.010402.49750.0998-0.1442.4215-0.66572.480412.41559.0365-64.6306
90-0.00420.0053-0.0259-0.00070.0101-0.0102-0.2378-0.01280.04110.2371-0.0604-0.03890.17740.24860.00022.64710.08230.44163.0320.59873.009522.676326.8852-74.7803
910.0067-0.0127-0.00020.00280.00040.0039-0.2632-0.13630.054-0.1492-0.1244-0.0989-0.0326-0.094202.47840.94280.65133.16310.20342.82628.346928.2835-65.7118
920.0091-0.0042-0.0019-0.00080.00760.00240.0381-0.189-0.0777-0.05540.09410.10480.0663-0.009802.43610.1760.37532.95210.18492.115626.458335.6577-52.3957
93-0.00350.0007-0.00190.0056-0.00080.0242-0.0027-0.04250.0853-0.05020.08610.04770.0670.079702.3956-0.24880.00032.36580.27991.955729.260738.1545-37.7523
940.0096-0.0001-0.0075-0.0033-0.01110.0070.0249-0.14440.1019-0.1032-0.3065-0.08780.01930.0628-02.5120.1876-0.17192.78010.44592.8828.639642.3355-24.5212
95-0.1903-0.3531-0.23540.1058-0.4894-0.04270.32810.26910.02660.02280.04170.6539-0.09220.0894-01.9659-0.1332-0.08792.50940.27962.426918.912-3.262-65.2264
960.0076-0.18790.09750.0572-0.06790.00980.3683-0.44830.001-0.36830.57680.38980.2474-0.52301.9228-0.0398-0.05092.54930.09992.503815.1709-28.762-55.729
970.0547-0.2161-0.0623-0.13020.06740.1927-0.1761-0.2438-0.4125-0.30160.4703-0.27910.1335-0.236501.7937-0.05950.03132.02390.04552.202337.7196-37.228-53.7904
98-0.00870.0861-0.1081-0.00690.02870.09111.90020.18111.00050.35520.5273-0.1740.93020.5475-00.53470.0858-0.6068-0.6575-2.2528-2.876748.9653-32.5488-32.1158
990.00750.00710.00590.0024-0.00080.00430.01510.0373-0.0188-0.1136-0.0646-0.0287-0.0185-0.0176-02.2398-0.2118-0.45471.8694-0.03712.147710.4345-21.9369-26.228
1000.0107-0.0063-0.0004-0.0004-0.00290.0097-0.16120.0728-0.0194-0.0752-0.1254-0.11520.0362-0.0427-01.8919-0.3645-0.31391.91850.28581.216618.4359-19.3788-29.0297
1010.00660.0027-0.0005-0.0012-0.00680.0001-0.1886-0.07820.01340.055-0.06530.0560.1891-0.0918-0.00011.86830.5361-0.2521.9829-0.38961.295717.0909-30.8464-27.8964
102-0.0288-0.06-0.07630.0118-0.0421-0.01080.17610.2108-0.10750.25410.3195-0.10440.00330.12102.63750.3843-0.48891.0812-0.05573.094731.6731-35.3511-42.2225
103-0.0251-0.00720.0192-0.004-0.0166-0.00120.17630.24340.06530.01860.1785-0.1141-0.0165-0.167102.1405-0.13080.01552.00560.13532.078725.8839-23.1751-60.3415
104-0.011-0.0110.01060.02390.02150.0040.17430.0497-0.12820.09830.0539-0.2277-0.0907-0.0992-02.8388-0.01860.09182.07960.06062.344421.4306-5.95-75.4651
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 164 )
2X-RAY DIFFRACTION2chain 'A' and (resid 165 through 248 )
3X-RAY DIFFRACTION3chain 'A' and (resid 249 through 367 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1864 through 1868 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1869 through 1877 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1878 through 1898 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1899 through 1903 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1904 through 1908 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1909 through 1913 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1914 through 1918 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1919 through 1924 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 164 )
13X-RAY DIFFRACTION13chain 'C' and (resid 165 through 367 )
14X-RAY DIFFRACTION14chain 'D' and (resid 1867 through 1905 )
15X-RAY DIFFRACTION15chain 'D' and (resid 1906 through 1915 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1916 through 1925 )
17X-RAY DIFFRACTION17chain 'E' and (resid 2 through 188 )
18X-RAY DIFFRACTION18chain 'E' and (resid 189 through 367 )
19X-RAY DIFFRACTION19chain 'F' and (resid 1870 through 1874 )
20X-RAY DIFFRACTION20chain 'F' and (resid 1875 through 1901 )
21X-RAY DIFFRACTION21chain 'F' and (resid 1902 through 1906 )
22X-RAY DIFFRACTION22chain 'F' and (resid 1907 through 1911 )
23X-RAY DIFFRACTION23chain 'F' and (resid 1912 through 1916 )
24X-RAY DIFFRACTION24chain 'F' and (resid 1917 through 1918 )
25X-RAY DIFFRACTION25chain 'F' and (resid 1919 through 1923 )
26X-RAY DIFFRACTION26chain 'F' and (resid 1924 through 1928 )
27X-RAY DIFFRACTION27chain 'G' and (resid 1 through 50 )
28X-RAY DIFFRACTION28chain 'G' and (resid 51 through 130 )
29X-RAY DIFFRACTION29chain 'G' and (resid 131 through 164 )
30X-RAY DIFFRACTION30chain 'G' and (resid 165 through 228 )
31X-RAY DIFFRACTION31chain 'G' and (resid 229 through 328 )
32X-RAY DIFFRACTION32chain 'G' and (resid 329 through 367 )
33X-RAY DIFFRACTION33chain 'H' and (resid 1869 through 1878 )
34X-RAY DIFFRACTION34chain 'H' and (resid 1879 through 1909 )
35X-RAY DIFFRACTION35chain 'H' and (resid 1910 through 1918 )
36X-RAY DIFFRACTION36chain 'H' and (resid 1919 through 1925 )
37X-RAY DIFFRACTION37chain 'I' and (resid 1 through 50 )
38X-RAY DIFFRACTION38chain 'I' and (resid 51 through 87 )
39X-RAY DIFFRACTION39chain 'I' and (resid 88 through 130 )
40X-RAY DIFFRACTION40chain 'I' and (resid 131 through 164 )
41X-RAY DIFFRACTION41chain 'I' and (resid 165 through 208 )
42X-RAY DIFFRACTION42chain 'I' and (resid 209 through 307 )
43X-RAY DIFFRACTION43chain 'I' and (resid 308 through 367 )
44X-RAY DIFFRACTION44chain 'J' and (resid 1866 through 1907 )
45X-RAY DIFFRACTION45chain 'J' and (resid 1908 through 1917 )
46X-RAY DIFFRACTION46chain 'J' and (resid 1918 through 1925 )
47X-RAY DIFFRACTION47chain 'K' and (resid 2 through 50 )
48X-RAY DIFFRACTION48chain 'K' and (resid 51 through 130 )
49X-RAY DIFFRACTION49chain 'K' and (resid 131 through 165 )
50X-RAY DIFFRACTION50chain 'K' and (resid 166 through 328 )
51X-RAY DIFFRACTION51chain 'K' and (resid 329 through 367 )
52X-RAY DIFFRACTION52chain 'L' and (resid 1864 through 1877 )
53X-RAY DIFFRACTION53chain 'L' and (resid 1878 through 1913 )
54X-RAY DIFFRACTION54chain 'L' and (resid 1914 through 1928 )
55X-RAY DIFFRACTION55chain 'M' and (resid 2 through 188 )
56X-RAY DIFFRACTION56chain 'M' and (resid 189 through 367 )
57X-RAY DIFFRACTION57chain 'N' and (resid 1867 through 1903 )
58X-RAY DIFFRACTION58chain 'N' and (resid 1904 through 1913 )
59X-RAY DIFFRACTION59chain 'N' and (resid 1914 through 1927 )
60X-RAY DIFFRACTION60chain 'O' and (resid 3 through 208 )
61X-RAY DIFFRACTION61chain 'O' and (resid 209 through 367 )
62X-RAY DIFFRACTION62chain 'P' and (resid 1867 through 1872 )
63X-RAY DIFFRACTION63chain 'P' and (resid 1873 through 1877 )
64X-RAY DIFFRACTION64chain 'P' and (resid 1878 through 1900 )
65X-RAY DIFFRACTION65chain 'P' and (resid 1901 through 1910 )
66X-RAY DIFFRACTION66chain 'P' and (resid 1911 through 1915 )
67X-RAY DIFFRACTION67chain 'P' and (resid 1916 through 1927 )
68X-RAY DIFFRACTION68chain 'Q' and (resid 1 through 164 )
69X-RAY DIFFRACTION69chain 'Q' and (resid 165 through 367 )
70X-RAY DIFFRACTION70chain 'R' and (resid 1867 through 1880 )
71X-RAY DIFFRACTION71chain 'R' and (resid 1902 through 1916 )
72X-RAY DIFFRACTION72chain 'R' and (resid 1917 through 1927 )
73X-RAY DIFFRACTION73chain 'S' and (resid 2 through 30 )
74X-RAY DIFFRACTION74chain 'S' and (resid 31 through 50 )
75X-RAY DIFFRACTION75chain 'S' and (resid 51 through 130 )
76X-RAY DIFFRACTION76chain 'S' and (resid 131 through 188 )
77X-RAY DIFFRACTION77chain 'S' and (resid 189 through 307 )
78X-RAY DIFFRACTION78chain 'S' and (resid 308 through 367 )
79X-RAY DIFFRACTION79chain 'T' and (resid 1866 through 1875 )
80X-RAY DIFFRACTION80chain 'T' and (resid 1876 through 1901 )
81X-RAY DIFFRACTION81chain 'T' and (resid 1902 through 1906 )
82X-RAY DIFFRACTION82chain 'T' and (resid 1907 through 1916 )
83X-RAY DIFFRACTION83chain 'T' and (resid 1917 through 1921 )
84X-RAY DIFFRACTION84chain 'T' and (resid 1922 through 1926 )
85X-RAY DIFFRACTION85chain 'U' and (resid 2 through 50 )
86X-RAY DIFFRACTION86chain 'U' and (resid 51 through 188 )
87X-RAY DIFFRACTION87chain 'U' and (resid 189 through 367 )
88X-RAY DIFFRACTION88chain 'V' and (resid 1867 through 1871 )
89X-RAY DIFFRACTION89chain 'V' and (resid 1872 through 1876 )
90X-RAY DIFFRACTION90chain 'V' and (resid 1877 through 1902 )
91X-RAY DIFFRACTION91chain 'V' and (resid 1903 through 1907 )
92X-RAY DIFFRACTION92chain 'V' and (resid 1908 through 1912 )
93X-RAY DIFFRACTION93chain 'V' and (resid 1913 through 1917 )
94X-RAY DIFFRACTION94chain 'V' and (resid 1918 through 1926 )
95X-RAY DIFFRACTION95chain 'W' and (resid 2 through 130 )
96X-RAY DIFFRACTION96chain 'W' and (resid 131 through 208 )
97X-RAY DIFFRACTION97chain 'W' and (resid 209 through 328 )
98X-RAY DIFFRACTION98chain 'W' and (resid 329 through 367 )
99X-RAY DIFFRACTION99chain 'X' and (resid 1866 through 1870 )
100X-RAY DIFFRACTION100chain 'X' and (resid 1871 through 1875 )
101X-RAY DIFFRACTION101chain 'X' and (resid 1876 through 1880 )
102X-RAY DIFFRACTION102chain 'X' and (resid 1881 through 1905 )
103X-RAY DIFFRACTION103chain 'X' and (resid 1906 through 1915 )
104X-RAY DIFFRACTION104chain 'X' and (resid 1916 through 1925 )

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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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