[English] 日本語
Yorodumi
- PDB-5wby: Crystal structure of mTOR(deltaN)-mLST8-PRAS40(beta-strand) complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wby
TitleCrystal structure of mTOR(deltaN)-mLST8-PRAS40(beta-strand) complex
Components
  • Proline-rich AKT1 substrate 1
  • Serine/threonine-protein kinase mTOR
  • Target of rapamycin complex subunit LST8
KeywordsTRANSFERASE / WD40 / PRAS40 beta / complex
Function / homology
Function and homology information


cardiac cell development / positive regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process / RNA polymerase III type 2 promoter sequence-specific DNA binding / T-helper 1 cell lineage commitment / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / TORC2 complex ...cardiac cell development / positive regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process / RNA polymerase III type 2 promoter sequence-specific DNA binding / T-helper 1 cell lineage commitment / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / TORC2 complex / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / regulation of lysosome organization / TORC1 complex / negative regulation of lysosome organization / negative regulation of cell size / regulation of osteoclast differentiation / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / Energy dependent regulation of mTOR by LKB1-AMPK / cellular response to nutrient / cellular response to L-leucine / regulation of autophagosome assembly / Amino acids regulate mTORC1 / Dengue virus modulates apoptosis / cellular response to methionine / TORC2 signaling / negative regulation of TOR signaling / neurotrophin TRK receptor signaling pathway / TORC1 signaling / cellular response to osmotic stress / AKT phosphorylates targets in the cytosol / MTOR signalling / inositol hexakisphosphate binding / anoikis / negative regulation of protein localization to nucleus / positive regulation of ubiquitin-dependent protein catabolic process / regulation of cell size / negative regulation of macroautophagy / Macroautophagy / Constitutive Signaling by AKT1 E17K in Cancer / behavioral response to pain / positive regulation of transcription by RNA polymerase III / positive regulation of protein kinase activity / protein kinase inhibitor activity / response to amino acid / neuronal action potential / TOR signaling / mTORC1-mediated signalling / HSF1-dependent transactivation / positive regulation of translational initiation / CD28 dependent PI3K/Akt signaling / positive regulation of TOR signaling / positive regulation of lipid biosynthetic process / positive regulation of epithelial to mesenchymal transition / protein serine/threonine kinase inhibitor activity / T cell costimulation / vascular endothelial cell response to laminar fluid shear stress / negative regulation of protein kinase activity / cellular response to nutrient levels / regulation of cellular response to heat / 'de novo' pyrimidine nucleobase biosynthetic process / regulation of macroautophagy / cytoskeleton organization / negative regulation of insulin receptor signaling pathway / phagocytic vesicle / endomembrane system / negative regulation of TORC1 signaling / regulation of neuron apoptotic process / positive regulation of glycolytic process / protein serine/threonine kinase activator activity / negative regulation of autophagy / cellular response to amino acid starvation / regulation of actin cytoskeleton organization / cellular response to amino acid stimulus / cellular response to starvation / Regulation of PTEN gene transcription / regulation of signal transduction by p53 class mediator / phosphatidylinositol 3-kinase/protein kinase B signal transduction / VEGFR2 mediated vascular permeability / non-specific protein-tyrosine kinase / TP53 Regulates Metabolic Genes / regulation of cell growth / non-membrane spanning protein tyrosine kinase activity / positive regulation of translation / phosphoprotein binding / response to nutrient levels / PML body / regulation of circadian rhythm / cellular response to insulin stimulus / Regulation of TP53 Degradation / PIP3 activates AKT signaling / nuclear envelope / positive regulation of cell growth / response to heat / ribosome binding / protein tyrosine kinase activity / cellular response to hypoxia / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells
Similarity search - Function
Proline-rich AKT1 substrate 1 protein / : / Proline-rich AKT1 substrate 1 / Proline-rich AKT1 substrate 1, N-terminal domain / Target of rapamycin complex subunit LST8 / Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR ...Proline-rich AKT1 substrate 1 protein / : / Proline-rich AKT1 substrate 1 / Proline-rich AKT1 substrate 1, N-terminal domain / Target of rapamycin complex subunit LST8 / Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / Rapamycin binding domain / : / Serine/threonine-protein kinase ATR-like, HEAT repeats / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Quinoprotein alcohol dehydrogenase-like superfamily / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / WD domain, G-beta repeat / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase mTOR / Proline-rich AKT1 substrate 1 / Target of rapamycin complex subunit LST8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPavletich, N.P. / Yang, H.
CitationJournal: Nature / Year: 2017
Title: Mechanisms of mTORC1 activation by RHEB and inhibition by PRAS40.
Authors: Haijuan Yang / Xiaolu Jiang / Buren Li / Hyo J Yang / Meredith Miller / Angela Yang / Ankita Dhar / Nikola P Pavletich /
Abstract: The mechanistic target of rapamycin complex 1 (mTORC1) controls cell growth and metabolism in response to nutrients, energy levels, and growth factors. It contains the atypical kinase mTOR and the ...The mechanistic target of rapamycin complex 1 (mTORC1) controls cell growth and metabolism in response to nutrients, energy levels, and growth factors. It contains the atypical kinase mTOR and the RAPTOR subunit that binds to the Tor signalling sequence (TOS) motif of substrates and regulators. mTORC1 is activated by the small GTPase RHEB (Ras homologue enriched in brain) and inhibited by PRAS40. Here we present the 3.0 ångström cryo-electron microscopy structure of mTORC1 and the 3.4 ångström structure of activated RHEB-mTORC1. RHEB binds to mTOR distally from the kinase active site, yet causes a global conformational change that allosterically realigns active-site residues, accelerating catalysis. Cancer-associated hyperactivating mutations map to structural elements that maintain the inactive state, and we provide biochemical evidence that they mimic RHEB relieving auto-inhibition. We also present crystal structures of RAPTOR-TOS motif complexes that define the determinants of TOS recognition, of an mTOR FKBP12-rapamycin-binding (FRB) domain-substrate complex that establishes a second substrate-recruitment mechanism, and of a truncated mTOR-PRAS40 complex that reveals PRAS40 inhibits both substrate-recruitment sites. These findings help explain how mTORC1 selects its substrates, how its kinase activity is controlled, and how it is activated by cancer-associated mutations.
History
DepositionJun 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Serine/threonine-protein kinase mTOR
D: Target of rapamycin complex subunit LST8
A: Serine/threonine-protein kinase mTOR
C: Target of rapamycin complex subunit LST8
P: Proline-rich AKT1 substrate 1
O: Proline-rich AKT1 substrate 1


Theoretical massNumber of molelcules
Total (without water)362,5116
Polymers362,5116
Non-polymers00
Water00
1
B: Serine/threonine-protein kinase mTOR
D: Target of rapamycin complex subunit LST8
P: Proline-rich AKT1 substrate 1


Theoretical massNumber of molelcules
Total (without water)181,2563
Polymers181,2563
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Serine/threonine-protein kinase mTOR
C: Target of rapamycin complex subunit LST8
O: Proline-rich AKT1 substrate 1


Theoretical massNumber of molelcules
Total (without water)181,2563
Polymers181,2563
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.926, 163.044, 206.666
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11B
21A
12B
22A
13B
23A
14B
24A
15B
25A
16B
26A
17B
27A
18B
28A
19B
29A
110B
210A
111B
211A
112B
212A
113B
213A
114B
214A
115B
215A
116B
216A
117D
217C
118P
218O

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLUGLUBA1385 - 144213 - 70
21GLUGLUGLUGLUAC1385 - 144213 - 70
12LEULEUVALVALBA1443 - 150471 - 132
22LEULEUVALVALAC1443 - 150471 - 132
13ASNASNPROPROBA1505 - 1537133 - 165
23ASNASNPROPROAC1505 - 1537133 - 165
14ARGARGGLYGLYBA1538 - 1580166 - 208
24ARGARGGLYGLYAC1538 - 1580166 - 208
15GLUGLUTYRTYRBA1581 - 1605209 - 233
25GLUGLUTYRTYRAC1581 - 1605209 - 233
16ARGARGGLYGLYBA1612 - 1678240 - 306
26ARGARGGLYGLYAC1612 - 1678240 - 306
17VALVALTHRTHRBA1679 - 1734307 - 362
27VALVALTHRTHRAC1679 - 1734307 - 362
18GLUGLULYSLYSBA1735 - 1814363 - 442
28GLUGLULYSLYSAC1735 - 1814363 - 442
19LYSLYSILEILEBA1867 - 1930495 - 558
29LYSLYSILEILEAC1867 - 1930495 - 558
110GLNGLNHISHISBA1931 - 2001559 - 629
210GLNGLNHISHISAC1931 - 2001559 - 629
111SERSERILEILEBA2002 - 2021630 - 649
211SERSERILEILEAC2002 - 2021630 - 649
112LEULEULEULEUBA2022 - 2115650 - 743
212LEULEULEULEUAC2022 - 2115650 - 743
113PROPROGLUGLUBA2116 - 2190744 - 818
213PROPROGLUGLUAC2116 - 2190744 - 818
114ASPASPASPASPBA2191 - 2212819 - 840
214ASPASPASPASPAC2191 - 2212819 - 840
115PROPROPROPROBA2213 - 2241841 - 869
215PROPROPROPROAC2213 - 2241841 - 869
116HISHISTRPTRPBA2242 - 2549870 - 1177
216HISHISTRPTRPAC2242 - 2549870 - 1177
117VALVALVALVALDB8 - 32410 - 326
217VALVALVALVALCD8 - 32410 - 326
118SERSERLYSLYSPE187 - 19678 - 87
218SERSERLYSLYSOF187 - 19678 - 87

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999973, -0.007384, 0.000186), (-0.007386, -0.999823, 0.017318), (5.8E-5, -0.017319, -0.99985)-69.721687, -31.5979, -102.920921
3given(1), (1), (1)
4given(0.999676, -0.012174, -0.022333), (-0.011942, -0.999873, 0.01051), (-0.022458, -0.01024, -0.999695)-71.616333, -31.80653, -100.876343
5given(1), (1), (1)
6given(0.999834, -0.006294, -0.017069), (-0.006308, -0.99998, -0.000781), (-0.017064, 0.000889, -0.999854)-70.896301, -33.261791, -100.962967
7given(1), (1), (1)
8given(0.999633, -0.020611, -0.017579), (-0.020801, -0.999726, -0.010739), (-0.017353, 0.011101, -0.999788)-71.454193, -33.158482, -100.762711
9given(1), (1), (1)
10given(0.999792, 0.004595, -0.019854), (0.004865, -0.999896, 0.013548), (-0.01979, -0.013642, -0.999711)-71.016693, -32.98035, -101.174683
11given(1), (1), (1)
12given(0.999847, 0.00743, -0.015861), (0.007578, -0.999928, 0.009288), (-0.015791, -0.009407, -0.999831)-70.589417, -33.776451, -101.101448
13given(1), (1), (1)
14given(0.99977, 0.020708, -0.005645), (0.020927, -0.998899, 0.041993), (-0.004769, -0.042101, -0.999102)-69.571709, -32.41103, -102.542084
15given(1), (1), (1)
16given(0.999949, 0.005613, -0.008454), (0.005913, -0.99934, 0.035846), (-0.008247, -0.035894, -0.999322)-69.747383, -31.27895, -102.332062
17given(1), (1), (1)
18given(0.999991, 0.003362, -0.00258), (0.00342, -0.999736, 0.022699), (-0.002503, -0.022708, -0.999739)-69.431091, -31.621099, -103.195023
19given(1), (1), (1)
20given(0.999986, 0.00479, -0.002046), (0.004825, -0.999835, 0.017532), (-0.001962, -0.017542, -0.999844)-69.400627, -31.935209, -103.386292
21given(1), (1), (1)
22given(0.99996, 0.008668, 0.002178), (0.008613, -0.999672, 0.024131), (0.002386, -0.024111, -0.999706)-69.312927, -31.887529, -103.477966
23given(1), (1), (1)
24given(0.999829, 0.013438, -0.012708), (0.013793, -0.999505, 0.028265), (-0.012322, -0.028436, -0.99952)-69.912338, -31.873739, -102.915489
25given(1), (1), (1)
26given(0.999966, 0.008156, 0.001065), (0.008131, -0.999718, 0.022324), (0.001247, -0.022315, -0.99975)-69.340233, -31.894831, -103.455849
27given(1), (1), (1)
28given(0.999999, 0.001063, 0.000381), (0.001052, -0.999588, 0.028693), (0.000411, -0.028693, -0.999588)-69.293953, -31.25392, -103.345261
29given(1), (1), (1)
30given(0.999959, 0.007712, -0.004753), (0.007873, -0.999364, 0.034765), (-0.004482, -0.034801, -0.999384)-69.590233, -31.381359, -102.991798
31given(1), (1), (1)
32given(0.999949, 0.010037, -0.000649), (0.010048, -0.999736, 0.020651), (-0.000442, -0.020657, -0.999786)-69.316872, -32.359402, -103.135262
33given(1), (1), (1)
34given(0.999955, 0.004915, 0.008095), (0.004914, -0.999988, 0.000132), (0.008095, -9.2E-5, -0.999967)-69.155327, -32.97868, -103.127113
35given(1), (1), (1)
36given(0.998327, -0.03443, 0.04646), (-0.03416, -0.999395, -0.006587), (0.046659, 0.004989, -0.998898)-69.001007, -29.43128, -106.350609

-
Components

#1: Protein Serine/threonine-protein kinase mTOR / FK506-binding protein 12-rapamycin complex-associated protein 1 / FKBP12-rapamycin complex- ...FK506-binding protein 12-rapamycin complex-associated protein 1 / FKBP12-rapamycin complex-associated protein / Mammalian target of rapamycin / mTOR / Mechanistic target of rapamycin / Rapamycin and FKBP12 target 1 / Rapamycin target protein 1


Mass: 134865.453 Da / Num. of mol.: 2 / Fragment: residues 1376-2549
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTOR, FRAP, FRAP1, FRAP2, RAFT1, RAPT1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: P42345, non-specific serine/threonine protein kinase
#2: Protein Target of rapamycin complex subunit LST8 / TORC subunit LST8 / G protein beta subunit-like / Protein GbetaL / Mammalian lethal with SEC13 ...TORC subunit LST8 / G protein beta subunit-like / Protein GbetaL / Mammalian lethal with SEC13 protein 8 / mLST8


Mass: 36054.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLST8, GBL, LST8 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9BVC4
#3: Protein Proline-rich AKT1 substrate 1 / 40 kDa proline-rich AKT substrate


Mass: 10336.045 Da / Num. of mol.: 2 / Fragment: residues 114-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKT1S1, PRAS40 / Plasmid: pET2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96B36

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 66.91 % / Mosaicity: 0.304 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: tacsimate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→80 Å / Num. obs: 71263 / % possible obs: 97.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.064 / Rrim(I) all: 0.131 / Χ2: 0.556 / Net I/σ(I): 4.6 / Num. measured all: 278987
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.1140.69271260.8260.3860.7980.55598.5
3.11-3.233.90.4750.8950.2690.550.56598.3
3.23-3.383.70.3380.9380.1990.3950.56896.9
3.38-3.563.90.2490.9640.1410.2880.55897.5
3.56-3.7840.1680.9820.0930.1930.55498.1
3.78-4.0740.110.990.0620.1280.55697.9
4.07-4.483.80.080.9940.0470.0940.5696.3
4.48-5.134.10.0790.9950.0440.0910.55597.2
5.13-6.463.90.070.9960.040.0810.55197.3
6.46-803.90.0330.9980.0190.0380.54194.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JSN

4jsn


Resolution: 3.1→50.01 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.903 / SU B: 54.095 / SU ML: 0.436 / Cross valid method: THROUGHOUT / ESU R Free: 0.522 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27587 1707 2.4 %RANDOM
Rwork0.23287 ---
obs0.2339 69072 82.54 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 98.723 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å2-0 Å2-0 Å2
2---4.64 Å20 Å2
3---5.54 Å2
Refinement stepCycle: 1 / Resolution: 3.1→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22243 0 0 0 22243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01922757
X-RAY DIFFRACTIONr_bond_other_d0.0010.0220893
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.94130849
X-RAY DIFFRACTIONr_angle_other_deg0.901348454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2952753
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15323.9631090
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33154008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.39615157
X-RAY DIFFRACTIONr_chiral_restr0.0640.23386
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0225139
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024662
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8692.32611045
X-RAY DIFFRACTIONr_mcbond_other2.8692.32611044
X-RAY DIFFRACTIONr_mcangle_it4.8924.64713787
X-RAY DIFFRACTIONr_mcangle_other4.8924.64813788
X-RAY DIFFRACTIONr_scbond_it2.9132.41311712
X-RAY DIFFRACTIONr_scbond_other2.9132.41311713
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.034.77217063
X-RAY DIFFRACTIONr_long_range_B_refined7.81151.85825048
X-RAY DIFFRACTIONr_long_range_B_other7.81151.86325049
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1010A419tight positional0.010.05
1111A120tight positional0.010.05
1212A556tight positional0.010.05
1313A439tight positional0.010.05
1414A131tight positional0.010.05
1515A169tight positional0.010.05
1616A1500tight positional0.010.05
1717C1866tight positional0.010.05
1818O58tight positional00.05
11A556medium positional0.010.5
22A627medium positional0.010.5
33A280medium positional0.010.5
44A387medium positional0.010.5
55A226medium positional0.010.5
66A727medium positional0.010.5
77A545medium positional0.010.5
88A816medium positional0.010.5
99A634medium positional0.010.5
1010A710medium positional0.010.5
1111A187medium positional0.010.5
1212A980medium positional0.010.5
1313A744medium positional0.010.5
1414A216medium positional0.010.5
1515A281medium positional0.010.5
1616A2552medium positional0.010.5
1717C2783medium positional0.010.5
1818O110medium positional0.010.5
11A342tight thermal3.1399
22A368tight thermal11.1299
33A195tight thermal12.0299
44A256tight thermal9.999
55A149tight thermal8.3299
66A397tight thermal6.7199
77A332tight thermal3.4399
88A477tight thermal3.599
99A378tight thermal2.4799
1010A419tight thermal2.7299
1111A120tight thermal2.9199
1212A556tight thermal12.5599
1313A439tight thermal4.0999
1414A131tight thermal2.999
1515A169tight thermal2.9399
1616A1500tight thermal3.9899
1717C1866tight thermal4.499
1818O58tight thermal7.5699
11A556medium thermal499
22A627medium thermal10.9899
33A280medium thermal11.0499
44A387medium thermal8.3299
55A226medium thermal10.0399
66A727medium thermal7.8999
77A545medium thermal3.8699
88A816medium thermal4.0999
99A634medium thermal2.9499
1010A710medium thermal3.8599
1111A187medium thermal3.1999
1212A980medium thermal11.3999
1313A744medium thermal3.7799
1414A216medium thermal4.1799
1515A281medium thermal3.2799
1616A2552medium thermal4.6599
1717C2783medium thermal4.8199
1818O110medium thermal7.899
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 54 -
Rwork0.355 2082 -
obs--34.31 %
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)
16.91882.2317-1.84.482-1.31525.0370.1887-0.79790.24980.459-0.3951-0.09-0.29850.44080.20640.68320.0299-0.02220.7121-0.17880.433-10.275-6-31.986
26.66370.9826-0.30920.5978-0.6460.8208-0.15-0.1480.55460.2836-0.1816-0.1564-0.43210.28470.33161.30880.0227-0.12011.0591-0.09230.869916.1380.423-25.046
32.3164-0.9105-1.87141.78570.65562.1282-0.0339-0.19440.22690.7175-0.10280.6135-0.154-0.59750.13671.0741-0.03030.05281.4255-0.22540.852412.902-18.662-12.3
44.52291.83831.09461.97130.70230.74340.09830.2456-0.0131-0.00770.0446-0.24790.14920.2465-0.1430.24860.05470.02360.20720.00870.130916.013-45.388-50.556
50.15170.04850.62120.33690.32943.6225-0.08110.31930.0233-0.51690.0145-0.4006-0.7610.51480.06661.1935-0.00920.1281.32030.23941.1276-27.647-43.279-84.499
60.82950.1078-0.01773.6122-0.99390.29960.0663-0.0117-0.172-0.1037-0.03460.2450.0724-0.0368-0.03160.1543-0.03780.01570.2428-0.00140.1669-13.443-27.796-53.928
74.8808-2.94881.42784.591-1.83544.66990.06540.7852-0.0216-0.5389-0.2808-0.0970.2340.37680.21530.8068-0.04110.04170.8006-0.11960.679859.466-27.236-70.954
82.48151.2762-0.58331.6814-1.8712.5736-0.09430.4745-0.497-0.37-0.0991-0.25540.63660.53560.19341.3390.16640.11721.2715-0.08831.079785.834-34.055-77.958
90.1427-0.04940.21570.1444-0.30180.8062-0.08080.1420.2501-0.17740.09190.14860.0395-0.2833-0.01111.3969-0.111-0.12461.6208-0.10481.401782.393-15.676-90.149
103.7748-1.7114-0.74222.31010.48890.73380.0388-0.24590.1722-0.02330.0692-0.1177-0.10230.2729-0.1080.2746-0.0632-0.06430.25650.01030.377185.41412.735-53.459
110.0518-0.00960.12710.2296-0.75613.37540.1392-0.20360.00370.24540.0110.03770.21290.2718-0.15031.49480.14830.16661.47010.01941.297342.07111.386-19.783
120.85180.2838-0.11093.7668-0.92130.2598-0.0026-0.02420.27110.15210.02220.187-0.0946-0.0492-0.01970.15460.04330.02850.2586-0.00710.455756.09-4.941-49.658
132.65950.14940.18324.09950.67943.8167-0.12350.4063-0.0032-0.40860.1485-0.2042-0.09730.0864-0.0250.2035-0.00110.0010.1172-0.0170.0135-1.2369.104-78.44
143.1985-0.0197-0.7113.75840.16053.4878-0.0732-0.7490.00690.68660.0676-0.5158-0.00460.20470.00560.34150.028-0.12240.2790.01590.404268.482-41.74-24.537
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1385 - 1442
2X-RAY DIFFRACTION2B1443 - 1504
3X-RAY DIFFRACTION3B1505 - 1678
4X-RAY DIFFRACTION4B1679 - 2021
5X-RAY DIFFRACTION5B2022 - 2115
6X-RAY DIFFRACTION6B2116 - 2459
7X-RAY DIFFRACTION7A1385 - 1442
8X-RAY DIFFRACTION8A1443 - 1504
9X-RAY DIFFRACTION9A1505 - 1678
10X-RAY DIFFRACTION10A1679 - 2021
11X-RAY DIFFRACTION11A2022 - 2115
12X-RAY DIFFRACTION12A2116 - 2459
13X-RAY DIFFRACTION13D8 - 324
14X-RAY DIFFRACTION13P187 - 196
15X-RAY DIFFRACTION14C8 - 324
16X-RAY DIFFRACTION14O187 - 196

+
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