[English] 日本語
Yorodumi
- PDB-4aj5: Crystal structure of the Ska core complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4aj5
TitleCrystal structure of the Ska core complex
Components
  • SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
  • SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
  • SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3
KeywordsCELL CYCLE / SKA COMPLEX / MITOSIS / CELL DIVISION / KINETOCHORE-MICROTUBULE ATTACHMENT / KMN NETWORK / NDC80 COMPLEX / DAM1/DASH
Function / homology
Function and homology information


negative regulation of mitotic spindle assembly checkpoint signaling / SKA complex / establishment of meiotic spindle orientation / metaphase chromosome alignment / mitotic spindle microtubule / outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / spindle assembly involved in female meiosis / meiotic spindle / mitotic metaphase chromosome alignment ...negative regulation of mitotic spindle assembly checkpoint signaling / SKA complex / establishment of meiotic spindle orientation / metaphase chromosome alignment / mitotic spindle microtubule / outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / spindle assembly involved in female meiosis / meiotic spindle / mitotic metaphase chromosome alignment / mitotic sister chromatid segregation / regulation of microtubule polymerization or depolymerization / intercellular bridge / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of microtubule polymerization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / spindle microtubule / chromosome segregation / RHO GTPases Activate Formins / kinetochore / centriolar satellite / mitotic spindle / Separation of Sister Chromatids / mitotic cell cycle / microtubule cytoskeleton / microtubule binding / ciliary basal body / cilium / cell division / centrosome / nucleoplasm / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1370 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1380 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1400 / Spindle and kinetochore-associated protein 2 / Spindle and kinetochore-associated protein 3 / Ska2, N-terminal / Spindle and kinetochore-associated protein 2 / Spindle and kinetochore-associated protein 1 / SKA1 microtubule binding domain / Spindle and kinetochore-associated protein 1 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1370 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1380 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1400 / Spindle and kinetochore-associated protein 2 / Spindle and kinetochore-associated protein 3 / Ska2, N-terminal / Spindle and kinetochore-associated protein 2 / Spindle and kinetochore-associated protein 1 / SKA1 microtubule binding domain / Spindle and kinetochore-associated protein 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Spindle and kinetochore-associated protein 3 / Spindle and kinetochore-associated protein 2 / SKA complex subunit 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.32 Å
AuthorsJeyaprakash, A.A. / Santamaria, A. / Jayachandran, U. / Chan, Y.W. / Benda, C. / Nigg, E.A. / Conti, E.
CitationJournal: Mol.Cell / Year: 2012
Title: Structural and Functional Organization of the Ska Complex, a Key Component of the Kinetochore-Microtubule Interface.
Authors: Jeyaprakash, A.A. / Santamaria, A. / Jayachandran, U. / Chan, Y.W. / Benda, C. / Nigg, E.A. / Conti, E.
History
DepositionFeb 15, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3
2: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3
3: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3
4: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3
A: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
B: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
C: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
D: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
E: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
F: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
G: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
H: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
I: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
J: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
K: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
L: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
M: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
N: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
O: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
P: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
Q: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
R: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
S: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
T: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
U: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3
V: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3
W: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3
X: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3
Y: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3
Z: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)367,17030
Polymers367,17030
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)174.400, 193.121, 198.267
Angle α, β, γ (deg.)90.00, 95.21, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
12
22
32
42
52
62
72
82
92
102
13
23
33
43
53
63
73
83
93
103

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN K AND (RESSEQ 1:28 OR RESSEQ 43:50)
211CHAIN L AND (RESSEQ 0:28 OR RESSEQ 43:50)
311CHAIN M AND (RESSEQ 0:28 OR RESSEQ 43:50)
411CHAIN N AND (RESSEQ 1:28 OR RESSEQ 43:50)
511CHAIN O AND (RESSEQ 0:28 OR RESSEQ 43:50)
611CHAIN P AND (RESSEQ 0:28 OR RESSEQ 43:50)
711CHAIN Q AND (RESSEQ 0:28 OR RESSEQ 44:50)
811CHAIN R AND (RESSEQ 0:28 OR RESSEQ 43:50)
911CHAIN S AND (RESSEQ 0:28 OR RESSEQ 43:50)
1011CHAIN T AND (RESSEQ 0:28 OR RESSEQ 43:50)
112CHAIN E AND (RESSEQ 4:60)
212CHAIN H AND (RESSEQ 4:60)
312CHAIN A AND (RESSEQ 4:60)
412CHAIN B AND (RESSEQ 4:60)
512CHAIN C AND (RESSEQ 4:60)
612CHAIN D AND (RESSEQ 4:60)
712CHAIN F AND (RESSEQ 4:60)
812CHAIN G AND (RESSEQ 4:60)
912CHAIN I AND (RESSEQ 4:60)
1012CHAIN J AND (RESSEQ 4:60)
113CHAIN U AND (RESSEQ 5:50)
213CHAIN V AND (RESSEQ 5:50)
313CHAIN W AND (RESSEQ 5:50)
413CHAIN X AND (RESSEQ 5:50)
513CHAIN Y AND (RESSEQ 5:50)
613CHAIN Z AND (RESSEQ 5:50)
713CHAIN 1 AND (RESSEQ 5:50)
813CHAIN 2 AND (RESSEQ 5:50)
913CHAIN 3 AND (RESSEQ 5:50)
1013CHAIN 4 AND (RESSEQ 5:50)

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.1914, 0.7366, 0.6486), (0.7442, -0.322, 0.5853), (0.64, 0.5947, -0.4865)-56.36, 32.14, 33.92
2given(-0.2229, -0.7075, 0.6706), (-0.7543, -0.3106, -0.5785), (0.6176, -0.6348, -0.4644)16.24, 101.7, 95.52
3given(-0.9048, -0.3976, 0.1523), (-0.424, 0.8154, -0.3936), (0.03233, -0.4208, -0.906)31.12, 32.31, 111.7
4given(0.1927, 0.02632, 0.9809), (-0.02054, -0.9993, 0.03085), (0.981, -0.0261, -0.1921)-39.46, 100.9, 48.26
5given(-0.8856, 0.4441, 0.136), (0.4601, 0.7991, 0.3869), (0.06315, 0.4052, -0.91)-9.809, -11.54, 68.96
6given(-0.08628, 0.4421, -0.8928), (-0.4823, -0.8027, -0.3509), (-0.8717, 0.4003, 0.282)31.01, 113.4, 22.56
7given(0.5748, 0.728, -0.372), (-0.7692, 0.3262, -0.5495), (-0.2791, 0.602, 0.7481)-15.39, 67.63, -15.27
8given(0.5685, -0.7583, -0.319), (0.7448, 0.3097, 0.5911), (-0.3494, -0.5736, 0.7409)57.83, 0.2538, 44.5
9given(-0.08726, -0.4771, -0.8745), (0.4658, -0.7955, 0.3875), (-0.8806, -0.3735, 0.2916)76.13, 68.01, 60.75
10given(0.1219, 0.05025, 0.9913), (-0.04582, -0.9974, 0.05619), (0.9915, -0.05227, -0.1192)-44.03, 98.22, 46.97
11given(0.5982, 0.7193, -0.3531), (-0.7446, 0.3363, -0.5766), (-0.296, 0.6078, 0.7368)-16.49, 68.58, -15.52
12given(0.5718, -0.7347, -0.365), (0.7673, 0.3216, 0.5548), (-0.2902, -0.5973, 0.7477)57.03, -0.2158, 45.98
13given(-0.1177, -0.4862, -0.8659), (0.4411, -0.8068, 0.3931), (-0.8897, -0.3357, 0.3094)75.98, 68.38, 58.52
14given(-0.1182, 0.464, -0.8779), (-0.4785, -0.8013, -0.3591), (-0.8701, 0.3776, 0.3167)28.62, 112.3, 22.32
15given(-0.8732, 0.4711, 0.1246), (0.4829, 0.8026, 0.3501), (0.06491, 0.3659, -0.9284)-12.04, -11.76, 72.73
16given(-0.2372, 0.7033, 0.6702), (0.7253, -0.3308, 0.6038), (0.6463, 0.6293, -0.4316)-57.65, 31.14, 30.32
17given(-0.2321, -0.6965, 0.679), (-0.7392, -0.3275, -0.5886), (0.6323, -0.6385, -0.4388)13.99, 102.4, 94.15
18given(-0.8795, -0.4546, 0.141), (-0.4725, 0.7986, -0.3728), (0.05684, -0.3945, -0.9171)33.35, 32.4, 110.7
19given(0.19, -0.0807, 0.9785), (0.0534, -0.9943, -0.09238), (0.9803, 0.0698, -0.1847)-32.52, 104.9, 41.27
20given(0.5858, 0.7285, -0.3551), (-0.7587, 0.3388, -0.5564), (-0.285, 0.5953, 0.7512)-16.47, 68.1, -16.29
21given(0.6419, -0.7234, -0.2542), (0.6622, 0.3558, 0.6595), (-0.3866, -0.5917, 0.7074)54.71, -5.761, 46.2
22given(-0.1189, -0.5304, -0.8394), (0.4059, -0.7975, 0.4465), (-0.9062, -0.2876, 0.3101)78.65, 65.7, 55.27
23given(-0.1202, 0.4662, -0.8764), (-0.4819, -0.7993, -0.3591), (-0.8679, 0.3792, 0.3208)28.43, 112.6, 21.96
24given(-0.8505, 0.5119, 0.1208), (0.5225, 0.7961, 0.3054), (0.06016, 0.3229, -0.9445)-12.54, -9.386, 74.84
25given(-0.0919, 0.6972, 0.711), (0.813, -0.3598, 0.4579), (0.575, 0.6201, -0.5337)-55.76, 38.67, 33.91
26given(-0.2424, -0.7147, 0.6561), (-0.7111, -0.3292, -0.6213), (0.66, -0.6172, -0.4284)17.11, 104.2, 91.54
27given(-0.8999, -0.4248, 0.09881), (-0.4236, 0.7971, -0.4304), (0.1041, -0.4291, -0.8972)35.78, 35.32, 109.7

-
Components

#1: Protein
SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3 / SKA3


Mass: 11842.551 Da / Num. of mol.: 10 / Fragment: RESIDUES 1-101 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): GOLD / References: UniProt: Q8IX90
#2: Protein
SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1 / SKA1


Mass: 10468.828 Da / Num. of mol.: 10 / Fragment: RESIDUES 1-91
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): GOLD / References: UniProt: Q96BD8
#3: Protein
SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2 / SKA2 / PROTEIN FAM33A


Mass: 14405.579 Da / Num. of mol.: 10 / Fragment: RESIDUES 1-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): GOLD / References: UniProt: Q8WVK7
Compound detailsENGINEERED RESIDUE IN CHAIN 1, VAL 58 TO ILE ENGINEERED RESIDUE IN CHAIN 2, VAL 58 TO ILE ...ENGINEERED RESIDUE IN CHAIN 1, VAL 58 TO ILE ENGINEERED RESIDUE IN CHAIN 2, VAL 58 TO ILE ENGINEERED RESIDUE IN CHAIN 3, VAL 58 TO ILE ENGINEERED RESIDUE IN CHAIN 4, VAL 58 TO ILE ENGINEERED RESIDUE IN CHAIN U, VAL 58 TO ILE ENGINEERED RESIDUE IN CHAIN V, VAL 58 TO ILE ENGINEERED RESIDUE IN CHAIN W, VAL 58 TO ILE ENGINEERED RESIDUE IN CHAIN X, VAL 58 TO ILE ENGINEERED RESIDUE IN CHAIN Y, VAL 58 TO ILE ENGINEERED RESIDUE IN CHAIN Z, VAL 58 TO ILE
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.93 Å3/Da / Density % sol: 75 %
Description: SE-MET DATA WERE USED TO CONFIRM SEQUENCE REGISTER
Crystal growpH: 7.6 / Details: 50 MM TRIS PH 7.6, 0.2 M LITHIUM ACETATE, 45% MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.3→86.8 Å / Num. obs: 91708 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 1.7 % / Biso Wilson estimate: 104.39 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 5.4
Reflection shellResolution: 3.3→3.5 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.2 / % possible all: 94.1

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.32→69.031 Å / SU ML: 0.56 / σ(F): 1.33 / Phase error: 35.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2797 4572 5 %
Rwork0.2345 --
obs0.2368 90812 94.22 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 89 Å2 / ksol: 0.276 e/Å3
Displacement parametersBiso mean: 140.2 Å2
Baniso -1Baniso -2Baniso -3
1-19.9554 Å20 Å2-53.9348 Å2
2---30.9808 Å20 Å2
3---11.0254 Å2
Refinement stepCycle: LAST / Resolution: 3.32→69.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21691 0 0 0 21691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921893
X-RAY DIFFRACTIONf_angle_d1.28129666
X-RAY DIFFRACTIONf_dihedral_angle_d17.3857921
X-RAY DIFFRACTIONf_chiral_restr0.0843634
X-RAY DIFFRACTIONf_plane_restr0.0053859
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11K296X-RAY DIFFRACTIONPOSITIONAL
12L296X-RAY DIFFRACTIONPOSITIONAL0.047
13M296X-RAY DIFFRACTIONPOSITIONAL0.045
14N296X-RAY DIFFRACTIONPOSITIONAL0.038
15O296X-RAY DIFFRACTIONPOSITIONAL0.046
16P296X-RAY DIFFRACTIONPOSITIONAL0.048
17Q289X-RAY DIFFRACTIONPOSITIONAL0.04
18R296X-RAY DIFFRACTIONPOSITIONAL0.049
19S288X-RAY DIFFRACTIONPOSITIONAL0.051
110T292X-RAY DIFFRACTIONPOSITIONAL0.04
21E435X-RAY DIFFRACTIONPOSITIONAL
22H435X-RAY DIFFRACTIONPOSITIONAL0.054
23A431X-RAY DIFFRACTIONPOSITIONAL0.039
24B439X-RAY DIFFRACTIONPOSITIONAL0.035
25C431X-RAY DIFFRACTIONPOSITIONAL0.036
26D435X-RAY DIFFRACTIONPOSITIONAL0.049
27F420X-RAY DIFFRACTIONPOSITIONAL0.047
28G439X-RAY DIFFRACTIONPOSITIONAL0.038
29I431X-RAY DIFFRACTIONPOSITIONAL0.045
210J431X-RAY DIFFRACTIONPOSITIONAL0.035
31U357X-RAY DIFFRACTIONPOSITIONAL
32V357X-RAY DIFFRACTIONPOSITIONAL0.041
33W357X-RAY DIFFRACTIONPOSITIONAL0.04
34X357X-RAY DIFFRACTIONPOSITIONAL0.042
35Y357X-RAY DIFFRACTIONPOSITIONAL0.042
36Z357X-RAY DIFFRACTIONPOSITIONAL0.041
371357X-RAY DIFFRACTIONPOSITIONAL0.04
382357X-RAY DIFFRACTIONPOSITIONAL0.061
393351X-RAY DIFFRACTIONPOSITIONAL0.041
3104357X-RAY DIFFRACTIONPOSITIONAL0.039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.32-3.35770.55761530.52552862X-RAY DIFFRACTION94
3.3577-3.39720.47421470.43962843X-RAY DIFFRACTION94
3.3972-3.43870.43381510.39362848X-RAY DIFFRACTION93
3.4387-3.48220.44921570.35992783X-RAY DIFFRACTION93
3.4822-3.5280.42021530.33642850X-RAY DIFFRACTION93
3.528-3.57630.41541340.32562789X-RAY DIFFRACTION93
3.5763-3.62740.37821360.33152882X-RAY DIFFRACTION93
3.6274-3.68160.34041670.31232813X-RAY DIFFRACTION94
3.6816-3.73910.39231410.29542952X-RAY DIFFRACTION95
3.7391-3.80040.31821520.27722859X-RAY DIFFRACTION95
3.8004-3.86590.32631560.26292863X-RAY DIFFRACTION94
3.8659-3.93620.29561460.26162906X-RAY DIFFRACTION95
3.9362-4.01190.31111530.24972828X-RAY DIFFRACTION95
4.0119-4.09380.32411330.23262910X-RAY DIFFRACTION95
4.0938-4.18280.2451530.21652856X-RAY DIFFRACTION94
4.1828-4.28010.27651430.20372849X-RAY DIFFRACTION94
4.2801-4.38710.23781700.18762827X-RAY DIFFRACTION93
4.3871-4.50570.24711440.18232860X-RAY DIFFRACTION93
4.5057-4.63820.26621300.18062893X-RAY DIFFRACTION95
4.6382-4.78790.26621720.19372874X-RAY DIFFRACTION95
4.7879-4.9590.22791410.18262932X-RAY DIFFRACTION95
4.959-5.15750.22741740.18422822X-RAY DIFFRACTION94
5.1575-5.39210.35171470.25042936X-RAY DIFFRACTION95
5.3921-5.67630.37081660.3082862X-RAY DIFFRACTION94
5.6763-6.03170.37811540.31672843X-RAY DIFFRACTION94
6.0317-6.49710.33251870.29992928X-RAY DIFFRACTION96
6.4971-7.15030.29651510.27652932X-RAY DIFFRACTION96
7.1503-8.18360.26271600.20912934X-RAY DIFFRACTION95
8.1836-10.30490.15041430.14042934X-RAY DIFFRACTION95
10.3049-69.04590.20681580.19922970X-RAY DIFFRACTION95
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)
12.113-0.5848-0.07971.4091-0.37430.13020.09750.6805-0.4521-0.4701-0.2618-0.12880.17170.2681-0.05570.27960.07420.39631.0059-0.17090.816317.759220.134836.7943
20.03410.0240.02670.03790.00070.03620.34160.32510.324-0.22650.51630.3662-0.3601-0.4812-0.00092.01440.2748-0.36451.81980.00151.36394.927223.299412.323
30.0387-0.06810.16030.1928-0.37560.70960.26870.1912-0.25150.1128-0.21320.7142-0.6929-0.15120.00341.50410.1308-0.49241.01930.15441.2213-34.068548.3666-4.5256
42.4047-2.52943.02152.5512-3.05873.54381.351-0.246-1.0898-1.17910.05881.10521.4481-0.60711.25760.9474-0.1759-0.06730.89380.17220.9991-17.510934.613413.0117
51.6388-0.750.46820.6915-0.58310.48730.29980.5437-0.4803-0.4964-0.23470.0063-0.13220.214-0.00430.992-0.0176-0.15420.6844-0.02250.6534-7.073933.734813.0288
60.0445-0.02850.02320.04540.00650.02930.3928-0.6960.1694-0.0690.9524-0.17-0.16421.21060.00562.38430.3902-0.40621.4723-0.18251.3247-46.128165.6886-15.9767
70.3311-0.0072-0.241.6208-0.36450.9697-0.4557-0.98940.21570.58090.38540.1118-0.3019-0.6954-0.00191.2690.0007-0.03431.1337-0.18010.62871.065781.319156.9525
80.9205-0.7551-0.07041.4521-0.65340.79-0.12790.17520.3378-0.6432-0.40421.360.0988-0.06380.00311.8866-0.2425-0.7911.15290.43672.139-38.908155.298824.6378
90.5256-0.5984-0.56894.28241.54320.83860.10620.08220.1097-0.0794-0.0466-0.2876-0.02040.04630.10221.49330.1921-1.07951.76950.02972.4123-58.790742.6523-4.4935
100.1560.0736-0.05310.0487-0.01830.0739-0.34420.19680.70740.80190.0909-0.15070.718-0.23190.00111.7933-0.2057-0.62151.2712-0.21771.6326-61.664552.2084-2.178
110.85290.15331.25520.40610.67641.74740.81710.1218-0.7026-0.366-0.4744-0.03740.81990.19551.66490.6361-0.25340.02740.70430.14940.970317.42898.576637.2014
120.92930.13220.57710.2231-0.18890.8249-0.30770.36930.8331-0.3962-0.04550.0797-0.33310.1666-0.79910.38710.0818-0.04160.19890.05650.1211-0.934980.247520.7938
130.69170.5816-0.93980.5257-0.74641.32810.1209-0.2938-0.4232-0.2867-0.7324-0.01770.3513-0.1756-0.2012.163-0.2806-1.09061.6523-0.32232.1098-6.442122.729918.188
140.4153-0.34330.01260.31710.13620.7899-0.06320.41290.0969-0.393-0.0867-0.3177-0.25470.3409-0.74860.9079-0.19950.36320.96130.12250.23086.048375.420625.1647
151.3780.0441.01731.92540.94972.3356-0.3431-0.09970.4881-0.0734-0.21210.5744-0.15410.2987-0.21830.5437-0.32970.25420.850.39870.689659.377690.474266.9274
160.0006-0.0240.02450.3522-0.21590.5349-0.0020.1620.1674-0.213-0.0797-0.2390.03510.2762-0.68810.8011-0.48470.32150.87880.53560.635434.045873.176147.1
170.8713-0.2624-0.22191.07161.06461.83610.26470.1962-0.70470.575-0.30960.06180.19840.38860.00060.6571-0.2021-0.41231.0541-0.00151.338556.363116.673266.377
180.0280.0325-0.04690.45370.1460.1763-0.404-0.1348-0.37260.2384-0.20290.36150.6883-0.2303-0.01771.3130.1132-0.48511.39860.24962.484278.6755-5.937979.8488
190.03970.04060.09220.2480.00230.2566-0.08910.014-0.25520.1997-0.17170.0504-0.38380.0436-0.13122.5461-0.2116-1.24240.9832-0.01642.649172.30337.288878.1107
200.47960.67320.64521.1881-0.33041.98570.4358-0.0762-0.35550.6084-0.0919-0.20170.47260.51020.2610.0698-0.29730.10130.01480.24580.199815.196319.63769.1948
210.484-0.2224-0.33130.75871.08561.5540.1375-0.08120.06680.00050.6101-0.0187-0.1348-0.00180.22681.35710.0609-0.63361.15010.33451.420464.0393-4.4901106.1195
220.2368-0.048-0.09540.04020.09940.2488-0.13270.2362-0.4772-0.0144-0.50440.33560.0441-0.1015-0.01691.3696-0.1613-0.63112.4105-0.34671.542150.5606-2.986395.4997
231.9185-1.1630.53750.7593-0.04291.7190.1773-0.6940.43380.6309-0.46140.903-0.2698-0.4083-0.00090.59780.06710.23810.957-0.16741.0641-22.127958.837840.3068
241.61580.51031.25081.20630.06221.7561-0.20110.0119-0.5986-0.97440.52620.0829-0.2270.5418-0.01020.522-0.2580.17560.7740.19150.8822-15.4692-9.90641.9802
251.84990.37180.33311.1739-0.21780.470.0272-0.97850.10170.53820.31590.17410.10330.0120.03631.3499-0.2292-0.1231.01590.29050.656424.368159.658475.3538
260.0011-0.0063-0.00670.03550.03750.0392-0.336-0.43170.3816-0.25790.64060.2096-0.0919-0.14390.00911.80190.1629-0.50051.36870.30061.64527.228482.6274.6067
270.19510.1769-0.02470.4119-0.26790.2044-0.2386-0.0822-0.03-0.2486-0.0152-0.125-0.5143-0.0203-0.00171.7366-0.0943-0.1811.0196-0.09061.4192-9.9969108.40743.6094
280.1317-0.0484-0.06190.0301-0.00440.08770.25841.05370.0101-0.29810.2174-0.3253-0.332-0.21650.09721.40820.2592-0.90721.2016-0.23531.7668-22.0307138.751732.5584
290.05160.04750.02330.04550.03380.0890.0434-0.3958-0.18280.6197-0.43630.50340.05231.1169-0.00042.2522-0.0256-1.20891.2110.12172.3042-11.4031130.370541.2917
301.56270.4544-0.82330.9116-0.07431.69120.0503-0.39610.00330.2369-0.0960.05070.05830.1331-0.06850.5649-0.50020.28390.81810.3770.485315.80927.482471.0768
311.06640.17420.8942.34330.21581.47920.19720.1418-0.69560.75650.5332-1.3166-0.06050.20140.01830.98320.11030.0020.8256-0.20280.491245.38988.39190.175
321.91511.07430.7160.98630.43430.2882-0.24610.70530.19-0.95680.33650.8208-0.31250.18050.10770.94620.0308-0.55890.50850.18710.8046-26.982568.21727.7461
330.71880.73271.60150.86631.82673.48470.808-0.0734-0.73360.9555-0.31690.03611.3811-0.10110.18180.5865-0.1354-0.13840.75490.13881.052618.15036.678542.2912
343.69892.325-0.99943.0027-0.31586.4469-0.38970.39590.2061-0.0870.7160.5999-0.5053-0.7311-1.74370.52-0.15380.29670.98430.11140.4305-12.447746.880127.6294
350.3476-0.156-0.08180.7906-0.26710.16150.07680.21540.6240.45610.24871.3127-0.3115-0.2854-0.05281.29090.1509-0.49960.62460.191.4278-5.612898.066217.3221
360.0305-0.00190.00850.03060.02250.01980.06630.37510.1460.0094-0.2880.05640.05450.139-0.00551.95880.1111-0.36881.26310.02311.6812.3205149.830422.4074
372.9494-0.1583-0.23210.6026-1.31122.93380.5751-0.34840.78690.9316-0.65310.5834-0.73720.1644-0.34560.64940.07080.43220.76280.09210.50391.637577.707937.1117
380.27-0.110.29390.2578-0.03580.3634-0.3149-0.68351.2552-0.4754-0.07510.6547-0.296-0.6699-0.00280.9094-0.06480.02130.85710.06331.038237.057491.756951.0067
390.18730.389-0.15056.38890.00030.14180.3863-0.5279-0.20990.8148-0.3829-0.993-0.06140.4285-0.63590.7111-0.3680.37530.9932-0.00520.708780.22595.963176.4888
401.2009-1.4172-0.08782.85010.85010.4899-0.2185-0.7169-0.31451.29160.5359-0.50290.47810.288-0.15450.9489-0.2868-0.14440.95570.18080.724548.461444.23564.5947
410.00520.0431-0.02350.4192-0.20270.1071-0.72570.1259-0.67530.0937-0.41010.11880.1619-0.0431-0.00251.82170.2169-0.59291.41040.33692.130277.1274-18.291271.5246
420.85020.43041.39470.34910.58012.36340.66980.0104-0.3830.2678-0.2118-0.61651.00180.75472.11690.4066-0.3235-0.03440.37160.35350.785521.588412.712369.4125
430.60791.05430.04151.75040.0219-0.0964-0.24460.1418-0.0131-1.65040.33870.12390.309-0.0425-0.00111.2736-0.2117-0.18890.72640.1080.8355-19.017514.427336.6647
442.9385-0.49810.91350.0534-0.08620.4753-0.41490.12781.6243-0.2653-0.3058-0.8917-0.5752-0.0163-1.27860.8773-0.3526-0.03580.63460.21060.58647.146295.227555.1868
450.2539-0.5973-0.0471.52320.77841.3379-0.2086-0.14520.1520.15770.6001-0.8197-0.27860.05440.9120.3639-0.05320.20360.64260.12160.199738.503664.488382.8722
461.26420.88480.63912.2427-0.51981.1879-0.2428-0.06840.24530.39830.1517-0.1155-0.1384-0.37310.00060.4667-0.14480.13490.78920.1280.6719-20.454518.278644.8904
470.78730.95270.53421.26020.36440.77180.0187-0.5614-0.2866-0.40180.04061.0477-0.3254-0.59860.01481.2687-0.0641-0.45720.97230.08311.7754-28.880166.669636.7514
480.880.82540.77170.81180.59711.25210.10840.5952-0.6153-0.9133-0.03810.45080.15180.5266-0.00180.94320.1604-0.24460.875-0.2281.283718.958.291434.6339
490.77940.4028-0.21281.40180.55030.4371-0.20970.34290.18220.158-0.1196-1.3181-0.6377-0.2714-0.00891.3877-0.1677-0.31090.8810.32950.9030.333880.272217.714
500.81240.3614-0.12270.281-0.09790.11830.07910.11720.0571-0.0152-0.1635-0.0934-0.24680.22221.40620.4002-0.30370.25780.71650.45370.327536.558283.108944.8316
510.0877-0.32270.04471.1909-0.16520.0230.074-0.2034-0.29590.74210.54360.24620.3325-0.2239-0.0441.4062-0.3259-0.82241.37870.34681.465878.453684.246381.8734
520.4399-0.171-0.7541.4725-0.6281.88650.36610.1772-1.4486-0.7785-0.09420.0791-0.1990.29520.00421.2569-0.2999-0.20940.81990.16531.16235.0762.798651.476
532.1230.84841.11281.57451.68031.8150.1118-0.0371-1.02290.13030.3484-0.45750.47750.45230.71860.1637-0.10490.07020.94320.2851.210759.904129.278260.2018
540.0204-0.0061-0.02990.00190.0090.04390.4747-0.1618-0.11850.28310.10090.2831-0.0096-0.34110.00491.57010.4645-0.26551.7503-0.31792.631463.4836-9.215868.5972
551.6955-0.26940.6940.26510.2040.73890.0658-0.4275-0.69870.477-0.024-0.23560.02030.11680.01450.9535-0.3636-0.43480.64450.36530.804713.03117.08571.9265
560.0060.01040.01360.01760.0230.0303-0.31960.51740.1679-0.73930.0118-0.58870.31410.35120.00152.1799-0.3158-1.04252.59770.87363.228560.333914.9828104.5331
571.6799-1.41180.61311.9503-1.46681.391-0.5459-0.42110.66380.3024-0.06560.2765-1.4022-0.0576-0.0521.604-0.0616-0.58770.6736-0.11961.31780.104193.350358.0206
580.98250.51160.35952.44370.82140.8781-0.0683-0.69990.19950.6098-0.2421-0.1614-0.0934-0.2964-0.00120.70470.05180.00890.8023-0.00150.64330.93164.375684.6207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN K AND (RESSEQ 1:32)
2X-RAY DIFFRACTION2CHAIN K AND (RESSEQ 33:43)
3X-RAY DIFFRACTION3CHAIN K AND (RESSEQ 44:113)
4X-RAY DIFFRACTION4CHAIN U
5X-RAY DIFFRACTION5CHAIN E AND (RESSEQ 3:79)
6X-RAY DIFFRACTION6CHAIN E AND (RESSEQ 80:88)
7X-RAY DIFFRACTION7CHAIN L AND (RESSEQ 0:42)
8X-RAY DIFFRACTION8CHAIN L AND (RESSEQ 43:85)
9X-RAY DIFFRACTION9CHAIN L AND (RESSEQ 86:91)
10X-RAY DIFFRACTION10CHAIN L AND (RESSEQ 92:113)
11X-RAY DIFFRACTION11CHAIN M
12X-RAY DIFFRACTION12CHAIN N AND (RESSEQ 1:104)
13X-RAY DIFFRACTION13CHAIN N AND (RESSEQ 105:114)
14X-RAY DIFFRACTION14CHAIN O AND (RESSEQ 0:41)
15X-RAY DIFFRACTION15CHAIN O AND (RESSEQ 42:114)
16X-RAY DIFFRACTION16CHAIN P AND (RESSEQ 0:42)
17X-RAY DIFFRACTION17CHAIN P AND (RESSEQ 43:95)
18X-RAY DIFFRACTION18CHAIN P AND (RESSEQ 96:103)
19X-RAY DIFFRACTION19CHAIN P AND (RESSEQ 104:113)
20X-RAY DIFFRACTION20CHAIN Q AND (RESSEQ 0:95)
21X-RAY DIFFRACTION21CHAIN Q AND (RESSEQ 96:103)
22X-RAY DIFFRACTION22CHAIN Q AND (RESSEQ 104:112)
23X-RAY DIFFRACTION23CHAIN R AND (RESSEQ 0:42)
24X-RAY DIFFRACTION24CHAIN R AND (RESSEQ 43:113)
25X-RAY DIFFRACTION25CHAIN S AND (RESSEQ -1:32)
26X-RAY DIFFRACTION26CHAIN S AND (RESSEQ 33:45)
27X-RAY DIFFRACTION27CHAIN S AND (RESSEQ 46:94)
28X-RAY DIFFRACTION28CHAIN S AND (RESSEQ 95:103)
29X-RAY DIFFRACTION29CHAIN S AND (RESSEQ 104:113)
30X-RAY DIFFRACTION30CHAIN T AND (RESSEQ 0:42)
31X-RAY DIFFRACTION31CHAIN T AND (RESSEQ 43:116)
32X-RAY DIFFRACTION32CHAIN V
33X-RAY DIFFRACTION33CHAIN W
34X-RAY DIFFRACTION34CHAIN X AND (RESSEQ 3:34)
35X-RAY DIFFRACTION35CHAIN X AND (RESSEQ 35:95)
36X-RAY DIFFRACTION36CHAIN X AND (RESSEQ 96:100)
37X-RAY DIFFRACTION37CHAIN Y AND (RESSEQ 3:34)
38X-RAY DIFFRACTION38CHAIN Y AND (RESSEQ 35:73)
39X-RAY DIFFRACTION39CHAIN Y AND (RESSEQ 74:101)
40X-RAY DIFFRACTION40CHAIN Z AND (RESSEQ 3:91)
41X-RAY DIFFRACTION41CHAIN Z AND (RESSEQ 92:99)
42X-RAY DIFFRACTION42CHAIN 1
43X-RAY DIFFRACTION43CHAIN 2
44X-RAY DIFFRACTION44CHAIN 3
45X-RAY DIFFRACTION45CHAIN 4
46X-RAY DIFFRACTION46CHAIN H
47X-RAY DIFFRACTION47CHAIN A
48X-RAY DIFFRACTION48CHAIN B
49X-RAY DIFFRACTION49CHAIN C
50X-RAY DIFFRACTION50CHAIN D AND (RESSEQ 3:79)
51X-RAY DIFFRACTION51CHAIN D AND (RESSEQ 80:88)
52X-RAY DIFFRACTION52CHAIN F AND (RESSEQ 3:32)
53X-RAY DIFFRACTION53CHAIN F AND (RESSEQ 33:79)
54X-RAY DIFFRACTION54CHAIN F AND (RESSEQ 80:84)
55X-RAY DIFFRACTION55CHAIN G AND (RESSEQ 3:77)
56X-RAY DIFFRACTION56CHAIN G AND (RESSEQ 78:88)
57X-RAY DIFFRACTION57CHAIN I
58X-RAY DIFFRACTION58CHAIN J

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • 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

-
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

Read more