[English] 日本語
Yorodumi
- PDB-5wbu: Crystal structure of mTOR(deltaN)-mLST8-PRAS40(alpha-helix & beta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wbu
TitleCrystal structure of mTOR(deltaN)-mLST8-PRAS40(alpha-helix & beta-strand) complex
Components
  • Proline-rich AKT1 substrate 1
  • Serine/threonine-protein kinase mTOR
  • Target of rapamycin complex subunit LST8MTOR
KeywordsTRANSFERASE / complex / FRB / WD40 / PRAS40
Function / homology
Function and homology information


RNA polymerase III type 2 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of pentose-phosphate shunt / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / TORC2 complex ...RNA polymerase III type 2 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of pentose-phosphate shunt / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / TORC2 complex / heart valve morphogenesis / regulation of membrane permeability / negative regulation of lysosome organization / RNA polymerase III type 3 promoter sequence-specific DNA binding / TORC1 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / calcineurin-NFAT signaling cascade / regulation of autophagosome assembly / TORC1 signaling / voluntary musculoskeletal movement / regulation of osteoclast differentiation / positive regulation of keratinocyte migration / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / cellular response to nutrient / energy reserve metabolic process / Energy dependent regulation of mTOR by LKB1-AMPK / nucleus localization / negative regulation of TOR signaling / ruffle organization / protein serine/threonine kinase inhibitor activity / negative regulation of cell size / cellular response to osmotic stress / anoikis / cardiac muscle cell development / positive regulation of transcription by RNA polymerase III / negative regulation of protein localization to nucleus / AKT phosphorylates targets in the cytosol / regulation of myelination / negative regulation of calcineurin-NFAT signaling cascade / Macroautophagy / regulation of cell size / negative regulation of macroautophagy / lysosome organization / positive regulation of oligodendrocyte differentiation / positive regulation of actin filament polymerization / protein kinase inhibitor activity / positive regulation of myotube differentiation / behavioral response to pain / TOR signaling / oligodendrocyte differentiation / mTORC1-mediated signalling / germ cell development / Constitutive Signaling by AKT1 E17K in Cancer / cellular response to nutrient levels / neurotrophin TRK receptor signaling pathway / CD28 dependent PI3K/Akt signaling / positive regulation of phosphoprotein phosphatase activity / positive regulation of translational initiation / neuronal action potential / HSF1-dependent transactivation / positive regulation of TOR signaling / positive regulation of epithelial to mesenchymal transition / regulation of macroautophagy / endomembrane system / 'de novo' pyrimidine nucleobase biosynthetic process / response to amino acid / positive regulation of lipid biosynthetic process / phagocytic vesicle / positive regulation of lamellipodium assembly / heart morphogenesis / regulation of neuron apoptotic process / regulation of cellular response to heat / cytoskeleton organization / cardiac muscle contraction / negative regulation of TORC1 signaling / positive regulation of stress fiber assembly / cellular response to amino acid starvation / T cell costimulation / cellular response to starvation / positive regulation of glycolytic process / protein serine/threonine kinase activator activity / response to nutrient levels / post-embryonic development / response to nutrient / negative regulation of autophagy / positive regulation of translation / VEGFR2 mediated vascular permeability / Regulation of PTEN gene transcription / regulation of signal transduction by p53 class mediator / regulation of cell growth / regulation of actin cytoskeleton organization / cellular response to amino acid stimulus / TP53 Regulates Metabolic Genes / macroautophagy / phosphoprotein binding / negative regulation of protein kinase activity / protein catabolic process / protein destabilization
Similarity search - Function
Proline-rich AKT1 substrate 1 protein / Proline-rich AKT1 substrate 1 / Target of rapamycin complex subunit LST8 / Domain of unknown function DUF3385, target of rapamycin protein / Domain of unknown function (DUF3385) / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain ...Proline-rich AKT1 substrate 1 protein / Proline-rich AKT1 substrate 1 / Target of rapamycin complex subunit LST8 / Domain of unknown function DUF3385, target of rapamycin protein / Domain of unknown function (DUF3385) / 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 / PIK-related kinase, FAT / FAT domain / FATC 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. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 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 / 7 Propeller / Methylamine Dehydrogenase; Chain H / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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: 3.42 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
P: Proline-rich AKT1 substrate 1
R: Proline-rich AKT1 substrate 1
A: Serine/threonine-protein kinase mTOR
C: Target of rapamycin complex subunit LST8
O: Proline-rich AKT1 substrate 1
Q: Proline-rich AKT1 substrate 1


Theoretical massNumber of molelcules
Total (without water)381,2318
Polymers381,2318
Non-polymers00
Water0
1
B: Serine/threonine-protein kinase mTOR
D: Target of rapamycin complex subunit LST8
P: Proline-rich AKT1 substrate 1
R: Proline-rich AKT1 substrate 1


Theoretical massNumber of molelcules
Total (without water)190,6164
Polymers190,6164
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
Q: Proline-rich AKT1 substrate 1


Theoretical massNumber of molelcules
Total (without water)190,6164
Polymers190,6164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.400, 163.200, 207.800
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
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
118R
218Q
119P
219O

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
21GLUGLUGLUGLUAE1385 - 144213 - 70
12LEULEUVALVALBA1443 - 150471 - 132
22LEULEUVALVALAE1443 - 150471 - 132
13ASNASNPROPROBA1505 - 1537133 - 165
23ASNASNPROPROAE1505 - 1537133 - 165
14ARGARGGLYGLYBA1538 - 1580166 - 208
24ARGARGGLYGLYAE1538 - 1580166 - 208
15GLUGLUTYRTYRBA1581 - 1605209 - 233
25GLUGLUTYRTYRAE1581 - 1605209 - 233
16ARGARGGLYGLYBA1612 - 1678240 - 306
26ARGARGGLYGLYAE1612 - 1678240 - 306
17VALVALTHRTHRBA1679 - 1734307 - 362
27VALVALTHRTHRAE1679 - 1734307 - 362
18GLUGLULYSLYSBA1735 - 1814363 - 442
28GLUGLULYSLYSAE1735 - 1814363 - 442
19LYSLYSILEILEBA1867 - 1930495 - 558
29LYSLYSILEILEAE1867 - 1930495 - 558
110GLNGLNHISHISBA1931 - 2001559 - 629
210GLNGLNHISHISAE1931 - 2001559 - 629
111SERSERILEILEBA2002 - 2021630 - 649
211SERSERILEILEAE2002 - 2021630 - 649
112LEULEULEULEUBA2022 - 2115650 - 743
212LEULEULEULEUAE2022 - 2115650 - 743
113PROPROGLUGLUBA2116 - 2190744 - 818
213PROPROGLUGLUAE2116 - 2190744 - 818
114ASPASPASPASPBA2191 - 2212819 - 840
214ASPASPASPASPAE2191 - 2212819 - 840
115PROPROPROPROBA2213 - 2241841 - 869
215PROPROPROPROAE2213 - 2241841 - 869
116HISHISTRPTRPBA2242 - 2549870 - 1177
216HISHISTRPTRPAE2242 - 2549870 - 1177
117VALVALVALVALDB8 - 32410 - 326
217VALVALVALVALCF8 - 32410 - 326
118SERSERASPASPRD212 - 23244 - 64
218SERSERASPASPQH212 - 23244 - 64
119VALVALLYSLYSPC188 - 19620 - 28
219VALVALLYSLYSOG188 - 19620 - 28

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999952, -0.006452, -0.007434), (-0.006293, -0.999755, 0.021207), (-0.007569, -0.02116, -0.999747)-70.40609, -31.20516, -103.282127
3given(1), (1), (1)
4given(0.999881, -0.012099, -0.009533), (-0.012017, -0.999891, 0.008577), (-0.009636, -0.008462, -0.999918)-70.932213, -31.787451, -102.569901
5given(1), (1), (1)
6given(0.999918, -0.000809, -0.012817), (-0.000721, -0.999976, 0.006834), (-0.012822, -0.006824, -0.999894)-70.769798, -32.959721, -102.205589
7given(1), (1), (1)
8given(0.999529, -0.021647, -0.02175), (-0.021886, -0.999702, -0.010812), (-0.021509, 0.011283, -0.999705)-72.343689, -32.981251, -101.049049
9given(1), (1), (1)
10given(0.999759, 0.012862, -0.017764), (0.013245, -0.999678, 0.021627), (-0.01748, -0.021857, -0.999608)-71.083099, -32.77993, -102.040283
11given(1), (1), (1)
12given(0.99986, 0.008484, -0.014415), (0.008658, -0.99989, 0.012052), (-0.014311, -0.012175, -0.999823)-70.726318, -33.37085, -101.938148
13given(1), (1), (1)
14given(0.999901, 0.013151, -0.005002), (0.01331, -0.999358, 0.033271), (-0.004561, -0.033334, -0.999434)-69.923073, -32.05603, -103.117783
15given(1), (1), (1)
16given(0.999986, 0.002948, -0.00442), (0.003072, -0.999601, 0.028092), (-0.004336, -0.028105, -0.999596)-69.830437, -31.368, -103.251266
17given(1), (1), (1)
18given(0.999985, 0.005472, -0.001062), (0.005485, -0.999907, 0.012502), (-0.000993, -0.012508, -0.999921)-69.711113, -32.341572, -103.876244
19given(1), (1), (1)
20given(0.99998, 0.00625, 0.000901), (0.006239, -0.999908, 0.012068), (0.000977, -0.012062, -0.999927)-69.607521, -32.361012, -104.055122
21given(1), (1), (1)
22given(0.999934, 0.011475, 0.001131), (0.011452, -0.999755, 0.018928), (0.001348, -0.018914, -0.99982)-69.759567, -32.296589, -103.876083
23given(1), (1), (1)
24given(0.999964, 0.006308, -0.0057), (0.006394, -0.999863, 0.015253), (-0.005603, -0.015289, -0.999867)-69.915047, -32.106339, -103.73645
25given(1), (1), (1)
26given(0.99999, 0.00447, -0.000378), (0.004475, -0.999864, 0.015861), (-0.000307, -0.015863, -0.999874)-69.645866, -32.019451, -103.898277
27given(1), (1), (1)
28given(0.999966, 0.007713, -0.003053), (0.007772, -0.999774, 0.01977), (-0.0029, -0.019793, -0.9998)-69.728683, -32.131081, -103.695267
29given(1), (1), (1)
30given(0.999986, 0.004219, -0.003198), (0.004293, -0.999717, 0.02342), (-0.003098, -0.023433, -0.999721)-69.766632, -31.729, -103.653816
31given(1), (1), (1)
32given(0.999981, 0.006093, -0.000411), (0.006098, -0.999864, 0.015329), (-0.000317, -0.015331, -0.999882)-69.596481, -32.302502, -103.754478
33given(1), (1), (1)
34given(0.999977, 0.003396, 0.005933), (0.003406, -0.999993, -0.001675), (0.005927, 0.001695, -0.999981)-69.471458, -32.899719, -103.675789
35given(1), (1), (1)
36given(0.999498, -0.028585, -0.01369), (-0.028154, -0.999133, 0.030664), (-0.014555, -0.030263, -0.999436)-70.18219, -30.542391, -103.488853
37given(1), (1), (1)
38given(0.999974, 0.004032, -0.005892), (0.003945, -0.999885, -0.014656), (-0.00595, 0.014632, -0.999875)-69.89402, -33.44083, -102.655777

-
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 / MTOR / 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: 9848.029 Da / Num. of mol.: 4 / Fragment: residues 173-256
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKT1S1, PRAS40 / 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: 3.27 Å3/Da / Density % sol: 66.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 8000

-
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: 3.4→80 Å / Num. obs: 61593 / % possible obs: 95.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.079 / Rrim(I) all: 0.158 / Χ2: 0.872 / Net I/σ(I): 4.5 / Num. measured all: 227760
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.4-3.522.80.59549754970.770.3860.7110.88486.5
3.52-3.662.80.5240.7970.350.6350.84990.5
3.66-3.832.80.3820.8950.2560.4630.88289.9
3.83-4.033.70.3390.940.1980.3950.87498
4.03-4.283.80.2370.9740.1360.2740.87998.3
4.28-4.6140.180.9830.0990.2070.90198.9
4.61-5.083.90.1460.9880.0810.1680.88397.5
5.08-5.814.40.1510.990.0790.1710.88399.2
5.81-7.324.20.1010.9950.0540.1150.89198.2
7.32-804.20.040.9990.0210.0450.80397.9

-
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: 3.42→50.01 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.904 / SU B: 74.876 / SU ML: 0.519 / Cross valid method: THROUGHOUT / ESU R Free: 0.651 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1305 2.5 %RANDOM
Rwork0.23455 ---
obs0.23531 51360 81.46 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 117.431 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å2-0 Å2
2---5.77 Å20 Å2
3---5.87 Å2
Refinement stepCycle: 1 / Resolution: 3.42→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22553 0 0 0 22553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01923067
X-RAY DIFFRACTIONr_bond_other_d0.0020.0221209
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.94231265
X-RAY DIFFRACTIONr_angle_other_deg1.003349176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97152791
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.86423.9421106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.571154066
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.93415163
X-RAY DIFFRACTIONr_chiral_restr0.070.23436
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0225477
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024722
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_it2.9652.56711203
X-RAY DIFFRACTIONr_mcbond_other2.9652.56711202
X-RAY DIFFRACTIONr_mcangle_it5.1035.12913981
X-RAY DIFFRACTIONr_mcangle_other5.1025.12913982
X-RAY DIFFRACTIONr_scbond_it2.8752.66411864
X-RAY DIFFRACTIONr_scbond_other2.8752.66411862
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1665.27417284
X-RAY DIFFRACTIONr_long_range_B_refined8.31356.90725354
X-RAY DIFFRACTIONr_long_range_B_other8.31256.90625354
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
1818Q125tight positional0.010.05
1919O52tight positional0.010.05
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
1818Q198medium positional0.010.5
1919O106medium positional0.010.5
11A342tight thermal2.799
22A368tight thermal6.8199
33A195tight thermal9.499
44A256tight thermal6.7799
55A149tight thermal8.4699
66A397tight thermal4.2999
77A332tight thermal3.7799
88A477tight thermal4.199
99A378tight thermal3.2899
1010A419tight thermal3.9399
1111A120tight thermal2.2899
1212A556tight thermal13.3899
1313A439tight thermal3.9699
1414A131tight thermal3.8299
1515A169tight thermal3.1699
1616A1500tight thermal4.0899
1717C1866tight thermal5.4199
1818Q125tight thermal15.8999
1919O52tight thermal2.9899
11A556medium thermal3.8299
22A627medium thermal6.4799
33A280medium thermal9.8899
44A387medium thermal6.6499
55A226medium thermal8.7299
66A727medium thermal4.9399
77A545medium thermal3.9299
88A816medium thermal4.9199
99A634medium thermal3.7399
1010A710medium thermal4.8799
1111A187medium thermal2.9999
1212A980medium thermal13.1899
1313A744medium thermal4.4599
1414A216medium thermal5.699
1515A281medium thermal3.2599
1616A2552medium thermal4.6599
1717C2783medium thermal6.0299
1818Q198medium thermal14.5399
1919O106medium thermal5.9499
LS refinement shellResolution: 3.422→3.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 64 -
Rwork0.412 2689 -
obs--58.26 %
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)
13.82111.1383-1.28998.1323-3.92083.90860.2861-0.87910.22170.3765-0.35940.2377-0.14210.48340.07340.9424-0.0293-0.06840.9922-0.17130.5704-10.1-6.034-32.213
25.86490.9112-0.45490.3628-0.38020.4731-0.0883-0.39820.34550.1139-0.2246-0.1797-0.24780.21270.31291.68980.0125-0.11051.3767-0.16931.203616.2510.525-25.35
31.30090.4575-1.40260.5105-0.37851.71510.0919-0.04240.22670.6809-0.13170.4163-0.0356-0.52660.03981.50280.12390.10321.9536-0.35741.458713.041-18.524-12.561
45.34312.14191.33122.32310.96541.14690.06170.3196-0.0874-0.08250.0924-0.39740.16740.3619-0.15420.30670.0950.06940.24550.03260.296116.041-45.468-50.568
50.64380.2731-1.33750.3113-1.27767.61530.12320.70820.1889-0.22580.16420.0167-0.5082-0.2384-0.28741.2328-0.023-0.09511.14970.03671.0178-28.046-40.601-84.504
61.19850.23230.00964.7903-1.26810.3940.06060.0512-0.1779-0.0462-0.05840.27440.0917-0.0594-0.00220.2152-0.07820.04440.2606-0.0370.2864-13.371-27.836-54.074
73.3438-1.02821.53326.0217-1.94195.21810.05211.04230.0558-0.5894-0.3192-0.22170.40560.3910.26710.9945-0.01330.07511.016-0.10090.907759.626-27.015-71.017
80.22110.05170.02270.1493-0.08980.07640.03150.4022-0.41060.0211-0.0386-0.06710.04110.20190.00711.6470.10380.15131.544-0.1341.394186.005-33.958-77.84
90.02610.0281-0.00130.1179-0.00570.0128-0.11620.13430.1131-0.45150.03910.08360.0217-0.11230.0771.8257-0.1614-0.14422.1673-0.36731.930782.641-15.585-90.076
104.9725-2.1658-1.27342.62530.75050.9991-0.0251-0.33050.17730.04360.1062-0.1128-0.1740.3422-0.08110.3313-0.0989-0.05210.28920.00830.544685.59312.832-53.441
110.1453-0.12260.4070.4369-1.4074.99570.143-0.3908-0.04820.14610.20290.04030.2175-0.2794-0.34591.50740.10910.12341.4621-0.04791.311341.6718.379-19.611
121.55820.2771-0.10914.8495-1.39240.42610.0087-0.11280.24120.09490.01530.2307-0.091-0.0543-0.02390.24450.07970.05670.2835-0.04060.646456.253-4.842-49.694
133.1833-0.05110.46765.38010.77694.8839-0.07920.46920.0151-0.51840.1257-0.271-0.04520.0858-0.04650.2311-0.00650.0020.1411-0.01070.0171-1.3349.097-78.589
144.1065-0.2385-0.98354.43680.2384.0778-0.1243-0.93850.00390.81530.0949-0.5236-0.04620.18950.02930.44250.0316-0.13940.32620.04150.541868.419-41.706-24.784
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 DIFFRACTION5R212 - 232
7X-RAY DIFFRACTION6B2116 - 2459
8X-RAY DIFFRACTION7A1385 - 1442
9X-RAY DIFFRACTION8A1443 - 1504
10X-RAY DIFFRACTION9A1505 - 1678
11X-RAY DIFFRACTION10A1679 - 2021
12X-RAY DIFFRACTION11A2022 - 2115
13X-RAY DIFFRACTION11Q212 - 232
14X-RAY DIFFRACTION12A2116 - 2459
15X-RAY DIFFRACTION13D8 - 324
16X-RAY DIFFRACTION13P188 - 196
17X-RAY DIFFRACTION14C8 - 324
18X-RAY DIFFRACTION14O188 - 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