[English] 日本語
Yorodumi
- PDB-7fql: Crystal Structure of human Legumain in complex with (2S)-N-[(1S)-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7fql
TitleCrystal Structure of human Legumain in complex with (2S)-N-[(1S)-3-amino-1-cyano-3-oxopropyl]-1-[1-[4-[(2,4-difluorophenyl)methoxy]phenyl]cyclopropanecarbonyl]pyrrolidine-2-carboxamide
ComponentsLegumain
KeywordsHYDROLASE / CYSTEINE PROTEASE / ALLOSTERIC INHIBITOR / ASPARAGINYL ENDOPEPTIDASE / ALZHEIMER'S DISEASE
Function / homology
Function and homology information


negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / receptor catabolic process / vitamin D metabolic process / self proteolysis / endolysosome lumen / response to acidic pH ...negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / receptor catabolic process / vitamin D metabolic process / self proteolysis / endolysosome lumen / response to acidic pH / activation of cysteine-type endopeptidase activity / dendritic spine organization / positive regulation of monocyte chemotaxis / Trafficking and processing of endosomal TLR / positive regulation of endothelial cell chemotaxis / negative regulation of multicellular organism growth / cellular response to hepatocyte growth factor stimulus / associative learning / protein maturation / endopeptidase activator activity / cellular response to calcium ion / MHC class II antigen presentation / positive regulation of mitotic cell cycle / lysosomal lumen / proteolysis involved in protein catabolic process / positive regulation of long-term synaptic potentiation / tau protein binding / memory / cellular response to amyloid-beta / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / apical part of cell / peptidase activity / negative regulation of neuron apoptotic process / lysosome / cysteine-type endopeptidase activity / negative regulation of gene expression / positive regulation of cell population proliferation / perinuclear region of cytoplasm / proteolysis / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
: / Legumain, prodomain / Legumain prodomain superfamily / Asparaginyl endopeptidase / Peptidase C13, legumain / Peptidase C13 family
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsEhler, A. / Benz, J. / Bartels, B. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche Switzerland
CitationJournal: To be published
Title: Crystal Structure of a human Legumain complex
Authors: Bartels, B. / Kuhn, B. / Benz, J. / Rudolph, M.G.
History
DepositionOct 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Legumain
B: Legumain
C: Legumain
D: Legumain
E: Legumain
F: Legumain
G: Legumain
H: Legumain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)414,83936
Polymers407,0218
Non-polymers7,81828
Water00
1
A: Legumain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5973
Polymers50,8781
Non-polymers7202
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Legumain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8974
Polymers50,8781
Non-polymers1,0193
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Legumain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6934
Polymers50,8781
Non-polymers8163
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Legumain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5973
Polymers50,8781
Non-polymers7202
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Legumain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1185
Polymers50,8781
Non-polymers1,2404
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Legumain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0116
Polymers50,8781
Non-polymers1,1335
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Legumain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0116
Polymers50,8781
Non-polymers1,1335
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Legumain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9155
Polymers50,8781
Non-polymers1,0374
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.301, 131.935, 117.677
Angle α, β, γ (deg.)90.000, 90.250, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Legumain / Asparaginyl endopeptidase / Protease / cysteine 1


Mass: 50877.672 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGMN, PRSC1 / Plasmid: pExpreS2.1_hLGMN(18-433)_C-VD-8xHis / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): ExpreS2 / References: UniProt: Q99538, legumain
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-WSN / N-[(2R)-4-amino-1-imino-4-oxobutan-2-yl]-1-(1-{4-[(2,4-difluorophenyl)methoxy]phenyl}cyclopropane-1-carbonyl)-L-prolinamide


Mass: 498.522 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C26H28F2N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.76 Å3/Da / Density % sol: 30.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 28.5mg/mL protein in 25mM HEPES/NaOH pH7, 300 mM NaCl, 200mM Trehalose incubated with 10-fold excess of ligand, then mixed 50-70% with 50-30% reservoir consisting of 20% v/v PEG smear broad, ...Details: 28.5mg/mL protein in 25mM HEPES/NaOH pH7, 300 mM NaCl, 200mM Trehalose incubated with 10-fold excess of ligand, then mixed 50-70% with 50-30% reservoir consisting of 20% v/v PEG smear broad, 0.1M MES/NaOH pH 6.5, total volume 200nL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.53→53.06 Å / Num. obs: 89638 / % possible obs: 99.1 % / Redundancy: 3.463 % / Biso Wilson estimate: 45.48 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.211 / Rrim(I) all: 0.25 / Χ2: 0.78 / Net I/σ(I): 4.18 / Num. measured all: 310382 / Scaling rejects: 139
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allCC1/2
2.53-2.63.5766.1770.2423832667566657.2799.9
2.6-2.673.555.60.322920648564576.59699.6
2.67-2.753.4964.10.422079632663164.84399.80.15
2.75-2.833.4173.6030.4620865611661074.2899.90.167
2.83-2.933.2742.3210.6819462595659452.78699.80.319
2.93-3.033.41.8980.8919624577557722.26199.90.405
3.03-3.143.6651.3511.2820452558655801.58899.90.666
3.14-3.273.6430.9581.8219407533653271.12899.80.727
3.27-3.423.6110.6282.6918443512451070.74199.70.844
3.42-3.583.5580.4363.617465492349080.51599.70.912
3.58-3.783.4840.3034.7716118466046260.35999.30.947
3.78-4.013.3820.2046.114932443844150.24299.50.973
4.01-4.283.1410.1427.4712851416540910.17298.20.983
4.28-4.633.3070.1119.4112469386037710.13397.70.988
4.63-5.073.5150.09211.1712201358834710.10996.70.992
5.07-5.673.490.08811.7210949322931370.10597.20.991
5.67-6.543.4520.083129647285727950.09897.80.99
6.54-8.013.150.06613.827393242023470.079970.993
8.01-11.333.2490.04917.965825189617930.05894.60.995
11.33-49.033.4210.0419.553448106010080.04795.10.997

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_4230refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2.53→49.03 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.4 / Stereochemistry target values: ML
Details: 10 chains in the a.u. ligand has different orientations of the terminal difluorophenyl group. Also some variations of the ether group conformations. THR146-147SNN peptide bond has bad ...Details: 10 chains in the a.u. ligand has different orientations of the terminal difluorophenyl group. Also some variations of the ether group conformations. THR146-147SNN peptide bond has bad geometry, despite meticulous parameterization in phenix.
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 2310 4.96 %RANDOM
Rwork0.192 44265 --
obs0.1949 46575 51.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.37 Å2 / Biso mean: 44.5462 Å2 / Biso min: 18.87 Å2
Refinement stepCycle: final / Resolution: 2.53→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16801 0 524 0 17325
Biso mean--47.96 --
Num. residues----2090
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.53-2.590.382130.343636391
2.59-2.650.4086140.32571711853
2.65-2.720.3048210.34474074288
2.72-2.790.2466360.314659663211
2.79-2.870.3951260.298977580114
2.87-2.960.3402460.30731004105019
2.96-3.070.4223850.31451445153027
3.07-3.190.38031010.28252491259246
3.19-3.340.32421520.24433123327559
3.34-3.510.30062160.22633667388369
3.51-3.730.29032210.20194155437677
3.74-4.020.23592380.18144773501189
4.02-4.430.22732740.160953875661100
4.43-5.070.20082800.149253975677100
5.07-6.380.22682880.186253945682100
6.38-49.030.24023090.189454445753100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.334-0.14980.0791.8563-0.72571.039-0.0652-0.14550.22860.19260.12120.2006-0.1590.05040.02060.2367-0.21530.08310.2344-0.04940.255176.415876.400294.3836
21.5184-0.02270.19650.90960.43791.6845-0.30980.09120.2029-0.13050.14380.1153-0.2844-0.010.01080.3346-0.0225-0.02430.15160.00130.330874.282480.652583.8756
31.1077-0.07430.05370.773-0.24371.0453-0.00230.270.3464-0.2342-0.0501-0.5409-0.22420.3190.03280.368-0.28660.08180.36120.02630.499988.573482.007180.5963
41.0327-0.1781-0.10571.25540.17720.2998-0.0513-0.23290.32210.29420.0277-0.3612-0.2720.2470.04640.4897-0.3289-0.06580.3888-0.13960.55191.514581.685496.5899
52.73351.0165-0.98635.1388-2.01692.207-0.04320.1009-0.0098-0.4890.2016-0.20280.17440.3705-0.16150.217-0.0312-0.00850.2829-0.03390.138388.93313.756199.0486
64.75781.88192.21994.22610.53431.96680.02380.7195-0.3344-0.45160.0453-0.2350.5319-0.1351-0.0430.4765-0.11970.02110.5547-0.07680.178484.39889.559392.3148
72.01220.4146-0.12431.8170.38971.20070.13120.2511-0.0055-0.42290.21790.07450.1104-0.0941-0.09440.4049-0.2172-0.28740.35740.07260.313375.89649.243102.1552
82.55290.63470.80530.46610.41431.14020.1283-0.5472-0.18380.17830.0304-0.15220.18390.1164-0.18910.382-0.1541-0.27660.46830.04820.409882.90945.6499117.9611
92.73160.3591-0.06681.5716-0.10681.95210.2399-0.2792-0.3568-0.1563-0.0786-0.17530.30780.1553-0.12370.3526-0.1507-0.2120.31730.08110.398779.90421.8988111.6835
101.2328-1.5612-0.62053.57431.17393.0159-0.11130.21030.2713-0.4139-0.0706-0.5319-0.21580.22330.13880.1906-0.0773-0.02650.28720.07160.243662.9558109.730264.3874
112.6369-0.18370.87465.49881.31614.3961-0.08670.21360.2306-0.3783-0.23260.0172-0.1291-0.05920.22430.2136-0.1420.0580.27960.06110.167161.0468102.526255.8656
121.6094-0.878-0.79872.0240.352.4115-0.1365-0.08910.240.0250.0175-0.1601-0.33140.0110.08980.299-0.0689-0.13040.27060.01770.213656.8743114.112773.603
132.7268-0.5063-1.81014.1114-1.22223.4273-0.28690.16790.2533-0.1956-0.1527-0.0633-0.1331-0.13260.20350.45440.1101-0.19250.3442-0.00510.177346.4668118.616870.1015
141.26270.60550.02620.3750.22420.68180.03350.0135-0.4926-0.05390.0720.04950.3712-0.19740.14690.2749-0.2052-0.07590.2102-0.07970.502965.232842.247377.0351
150.9304-0.3293-0.10840.3317-0.31430.594-0.05120.1025-0.18270.0167-0.01870.27650.1502-0.17730.06140.2851-0.2185-0.03660.176-0.00660.411958.124854.805478.9878
166.1916-0.89282.88311.384-0.80652.1143-0.0755-0.148-0.1257-0.07810.08410.1290.0597-0.1858-0.00280.4739-0.06480.1810.18370.06590.317264.284947.241681.9154
173.1476-1.42332.2350.9481-1.8145.42660.00220.0551-0.5330.1617-0.038-0.5835-0.21830.37610.05280.2947-0.0906-0.08910.2535-0.08390.485681.457540.938382.7288
180.16930.2364-0.24632.3501-0.08982.23120.18650.0006-0.47530.4216-0.1188-0.40270.35530.2904-0.00930.31530.0011-0.08270.1709-0.07740.362375.417441.308376.5131
192.31541.21581.23154.35971.12391.66040.1660.1588-0.69090.19790.0814-0.56020.22960.2003-0.27080.5024-0.05820.01270.3119-0.25020.449682.214236.358572.2394
201.1419-1.49110.18554.6081-0.12670.978-0.05350.181-0.0995-0.7660.111-0.3060.29680.1003-0.29060.5115-0.10080.00920.381-0.29990.485678.198840.532561.8508
211.3908-0.0884-1.77212.73030.48052.31010.02240.683-0.16720.09520.18070.22260.2553-0.0968-0.0720.3613-0.0835-0.18070.3523-0.09970.434460.160755.610165.7802
220.15340.4880.10611.5620.19011.11350.05640.3038-0.4527-0.23210.2115-0.18010.4590.0114-0.07660.5563-0.2464-0.07480.4408-0.27850.650861.350536.579761.7991
230.15030.18250.04421.26470.39081.36620.05830.1763-0.3096-0.23520.043-0.08730.30010.0176-0.06760.4926-0.1247-0.05390.3999-0.34450.596869.303533.641562.3662
240.8107-0.1482-0.01940.8558-0.81230.85910.07870.43260.0427-0.5190.0994-0.06820.20170.09820.02080.5645-0.18720.09990.5144-0.03630.098465.677769.460244.6314
250.4822-0.38930.34461.098-0.03770.31590.02950.38270.0958-0.66420.1361-0.32860.42680.295-0.04140.628-0.08440.13560.6756-0.08780.222773.266864.741742.6502
260.7094-0.20840.14240.64070.29981.11270.06620.32770.0653-0.3133-0.0491-0.25870.02440.23820.16160.4005-0.16120.18010.492-0.04040.202878.287267.236147.6749
271.3942-0.0361-1.50622.7162-2.01343.17860.03520.2348-0.2251-0.6257-0.0812-1.08880.33950.66570.06390.45030.03430.10430.6446-0.1110.537587.181564.461453.7284
282.79730.09410.12253.0628-0.48341.92510.21610.09640.3246-0.104-0.1043-0.59590.03920.4404-0.09560.4092-0.08850.17310.4635-0.08990.293383.492473.257556.104
291.8829-0.03820.06081.2257-0.15352.1796-0.0724-0.240.10720.16470.0511-0.07040.0857-0.1191-0.05340.6093-0.10370.07950.2994-0.04070.178567.130771.254761.6085
301.4718-0.00940.13130.9965-0.31441.4515-0.12840.3610.206-0.22080.0328-0.2256-0.23560.15280.11610.3205-0.11160.06670.34650.02290.203168.938380.399857.4577
311.78060.6768-2.45340.6858-0.47333.8715-0.15410.91990.6283-0.4188-0.08880.0936-0.19420.28930.14430.9479-0.03930.25760.58670.15180.50777.207186.446842.9389
321.2916-0.6950.17131.6721-0.86390.4813-0.37060.13660.19870.35930.114-0.8407-0.12180.17930.10020.2839-0.1039-0.13690.4855-0.10990.6339108.552552.3896100.8394
331.22410.31530.18430.7677-0.84191.4525-0.10780.11660.22750.12660.19-0.3997-0.10210.45230.09890.3266-0.0309-0.26580.5525-0.150.8369111.045555.0291101.6451
341.1192-0.3921-0.04990.8507-0.24021.7487-0.12290.31110.2286-0.2557-0.1548-0.7515-0.16040.52770.22310.7278-0.43530.29090.79590.0190.9863114.285359.618183.3633
350.71350.30280.05470.499-0.25881.025-0.0920.210.0686-0.1845-0.0453-0.605-0.070.47880.02460.2246-0.23690.18890.4824-0.09750.6367108.721454.947587.7411
361.3816-1.1099-0.51021.7553-0.17720.7352-0.09730.3040.3166-0.98970.0449-0.70650.00460.1278-0.00440.5167-0.22640.15210.4582-0.03850.5776106.736251.988778.379
370.8356-0.02750.02372.086-0.10941.1295-0.07120.01970.1638-0.24160.2434-0.3789-0.04520.2251-0.10340.2243-0.120.05080.3119-0.05210.326297.138144.368591.9
380.86180.52320.00510.58610.70571.9824-0.0265-0.08690.00080.2180.14350.5436-0.103-0.3861-0.24710.3572-0.05180.23690.35930.13880.714939.030679.551182.5276
391.90810.7767-0.36010.70980.73242.0296-0.10630.10960.3262-0.0892-0.18860.6530.0235-0.91320.22090.2716-0.0872-0.04130.76940.10510.971634.54183.858369.747
400.70270.68730.35171.28510.85811.80630.23210.19670.43050.2493-0.06570.57560.0951-0.8969-0.16360.4283-0.22610.16120.65480.05651.048734.333483.037678.4823
412.4926-0.1027-0.88420.28040.02341.939-0.1328-0.29380.06260.20920.17920.24690.0346-0.3119-0.06180.48390.03580.40810.5231-0.00610.72436.882388.028396.0252
421.6439-0.33820.11571.9309-0.8631.58630.0184-0.23230.17250.74240.06230.2882-0.2085-0.0674-0.09030.4584-0.07620.21810.28140.01290.384951.379986.235590.9842
433.2245-0.17530.74674.0942-1.40492.9835-0.02440.449-0.0489-0.0910.11970.71360.2026-0.3193-0.13620.388-0.0868-0.10180.29330.06880.360348.082182.088866.9153
440.66850.24570.06460.8359-0.16080.5798-0.0285-0.0448-0.26150.29230.06370.24390.2545-0.261-0.14340.5435-0.21530.13720.20520.09710.511252.981671.366384.3985
451.9045-0.1804-1.07791.15250.56191.0935-0.1535-0.252-0.00560.45160.30890.35180.2261-0.09050.37020.7540.06040.42580.39060.15050.491768.696442.0629119.4782
460.71760.6580.41280.88580.11910.45380.072-0.3591-0.16780.4743-0.04260.48190.1028-0.2827-0.06540.78830.05280.50690.47270.22380.872260.678335.9218119.2679
471.48850.1505-0.1171.16070.10170.198-0.1688-0.0977-0.1850.50240.21830.71130.009-0.21250.07690.3922-0.10030.30080.31780.1770.761462.54137.6095106.3625
481.52370.0547-0.41143.0716-0.08391.1802-0.142-0.15960.0010.0910.38560.9116-0.0869-0.195-0.16660.3866-0.05990.16380.23080.0910.498766.867751.3817103.1066
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 89 )A27 - 89
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 139 )A90 - 139
3X-RAY DIFFRACTION3chain 'A' and (resid 140 through 203 )A140 - 203
4X-RAY DIFFRACTION4chain 'A' and (resid 204 through 286 )A204 - 286
5X-RAY DIFFRACTION5chain 'B' and (resid 26 through 89 )B26 - 89
6X-RAY DIFFRACTION6chain 'B' and (resid 90 through 124 )B90 - 124
7X-RAY DIFFRACTION7chain 'B' and (resid 125 through 241 )B125 - 241
8X-RAY DIFFRACTION8chain 'B' and (resid 242 through 261 )B242 - 261
9X-RAY DIFFRACTION9chain 'B' and (resid 262 through 290 )B262 - 290
10X-RAY DIFFRACTION10chain 'C' and (resid 27 through 79 )C27 - 79
11X-RAY DIFFRACTION11chain 'C' and (resid 80 through 99 )C80 - 99
12X-RAY DIFFRACTION12chain 'C' and (resid 100 through 260 )C100 - 260
13X-RAY DIFFRACTION13chain 'C' and (resid 261 through 287 )C261 - 287
14X-RAY DIFFRACTION14chain 'D' and (resid 27 through 70 )D27 - 70
15X-RAY DIFFRACTION15chain 'D' and (resid 71 through 90 )D71 - 90
16X-RAY DIFFRACTION16chain 'D' and (resid 91 through 109 )D91 - 109
17X-RAY DIFFRACTION17chain 'D' and (resid 110 through 124 )D110 - 124
18X-RAY DIFFRACTION18chain 'D' and (resid 125 through 158 )D125 - 158
19X-RAY DIFFRACTION19chain 'D' and (resid 159 through 186 )D159 - 186
20X-RAY DIFFRACTION20chain 'D' and (resid 187 through 213 )D187 - 213
21X-RAY DIFFRACTION21chain 'D' and (resid 214 through 231 )D214 - 231
22X-RAY DIFFRACTION22chain 'D' and (resid 232 through 261 )D232 - 261
23X-RAY DIFFRACTION23chain 'D' and (resid 262 through 286 )D262 - 286
24X-RAY DIFFRACTION24chain 'E' and (resid 27 through 89 )E27 - 89
25X-RAY DIFFRACTION25chain 'E' and (resid 90 through 124 )E90 - 124
26X-RAY DIFFRACTION26chain 'E' and (resid 125 through 158 )E125 - 158
27X-RAY DIFFRACTION27chain 'E' and (resid 159 through 175 )E159 - 175
28X-RAY DIFFRACTION28chain 'E' and (resid 176 through 203 )E176 - 203
29X-RAY DIFFRACTION29chain 'E' and (resid 204 through 223 )E204 - 223
30X-RAY DIFFRACTION30chain 'E' and (resid 224 through 277 )E224 - 277
31X-RAY DIFFRACTION31chain 'E' and (resid 278 through 290 )E278 - 290
32X-RAY DIFFRACTION32chain 'F' and (resid 27 through 89 )F27 - 89
33X-RAY DIFFRACTION33chain 'F' and (resid 90 through 109 )F90 - 109
34X-RAY DIFFRACTION34chain 'F' and (resid 110 through 124 )F110 - 124
35X-RAY DIFFRACTION35chain 'F' and (resid 125 through 159 )F125 - 159
36X-RAY DIFFRACTION36chain 'F' and (resid 160 through 186 )F160 - 186
37X-RAY DIFFRACTION37chain 'F' and (resid 187 through 286 )F187 - 286
38X-RAY DIFFRACTION38chain 'G' and (resid 27 through 69 )G27 - 69
39X-RAY DIFFRACTION39chain 'G' and (resid 70 through 89 )G70 - 89
40X-RAY DIFFRACTION40chain 'G' and (resid 90 through 109 )G90 - 109
41X-RAY DIFFRACTION41chain 'G' and (resid 110 through 139 )G110 - 139
42X-RAY DIFFRACTION42chain 'G' and (resid 140 through 213 )G140 - 213
43X-RAY DIFFRACTION43chain 'G' and (resid 214 through 231 )G214 - 231
44X-RAY DIFFRACTION44chain 'G' and (resid 232 through 286 )G232 - 286
45X-RAY DIFFRACTION45chain 'H' and (resid 27 through 90 )H27 - 90
46X-RAY DIFFRACTION46chain 'H' and (resid 91 through 124 )H91 - 124
47X-RAY DIFFRACTION47chain 'H' and (resid 125 through 231 )H125 - 231
48X-RAY DIFFRACTION48chain 'H' and (resid 232 through 286 )H232 - 286

+
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://pdbjlvh1.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