[English] 日本語
Yorodumi
- PDB-3mxb: Molecular basis of engineered meganuclease targeting of the endog... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mxb
TitleMolecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus
Components
  • DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*GP*AP*GP*AP*AP*CP*AP*A)-3')
  • DNA (5'-D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*CP*CP*TP*CP*AP*GP*CP*CP*AP*GP*A)-3')
  • V2(K7E-G19S)
  • V3(E8K)
KeywordsHYDROLASE/DNA / PROTEIN-DNA COMPLEX / HYDROLASE-DNA complex
Function / homologyHoming endonucleases / Endonuclease I-creI / Roll / Alpha Beta / PHOSPHATE ION / DNA / DNA (> 10)
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMunoz, I.G. / Prieto, J. / Subramanian, S. / Coloma, J. / Montoya, G.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus.
Authors: Munoz, I.G. / Prieto, J. / Subramanian, S. / Coloma, J. / Redondo, P. / Villate, M. / Merino, N. / Marenchino, M. / D'Abramo, M. / Gervasio, F.L. / Grizot, S. / Daboussi, F. / Smith, J. / ...Authors: Munoz, I.G. / Prieto, J. / Subramanian, S. / Coloma, J. / Redondo, P. / Villate, M. / Merino, N. / Marenchino, M. / D'Abramo, M. / Gervasio, F.L. / Grizot, S. / Daboussi, F. / Smith, J. / Chion-Sotinel, I. / Paques, F. / Duchateau, P. / Alibes, A. / Stricher, F. / Serrano, L. / Blanco, F.J. / Montoya, G.
History
DepositionMay 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: V3(E8K)
B: V2(K7E-G19S)
C: DNA (5'-D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*CP*CP*TP*CP*AP*GP*CP*CP*AP*GP*A)-3')
E: DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*GP*AP*GP*AP*AP*CP*AP*A)-3')
R: V3(E8K)
S: V2(K7E-G19S)
T: DNA (5'-D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*CP*CP*TP*CP*AP*GP*CP*CP*AP*GP*A)-3')
V: DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*GP*AP*GP*AP*AP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,65816
Polymers109,1188
Non-polymers5408
Water3,225179
1
A: V3(E8K)
B: V2(K7E-G19S)
C: DNA (5'-D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*CP*CP*TP*CP*AP*GP*CP*CP*AP*GP*A)-3')
E: DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*GP*AP*GP*AP*AP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9249
Polymers54,5594
Non-polymers3655
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12050 Å2
ΔGint-122 kcal/mol
Surface area16700 Å2
MethodPISA
2
R: V3(E8K)
S: V2(K7E-G19S)
T: DNA (5'-D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*CP*CP*TP*CP*AP*GP*CP*CP*AP*GP*A)-3')
V: DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*GP*AP*GP*AP*AP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7347
Polymers54,5594
Non-polymers1753
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11570 Å2
ΔGint-106 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.050, 89.360, 86.340
Angle α, β, γ (deg.)90.00, 99.51, 90.00
Int Tables number4
Space group name H-MP1211
Details1

-
Components

-
Protein , 2 types, 4 molecules ARBS

#1: Protein V3(E8K)


Mass: 19992.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Plasmid: pET24d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
#2: Protein V2(K7E-G19S)


Mass: 19826.590 Da / Num. of mol.: 2 / Mutation: K7E,G19S,E8K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Plasmid: pET24d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS

-
DNA chain , 2 types, 4 molecules CTEV

#3: DNA chain DNA (5'-D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*CP*CP*TP*CP*AP*GP*CP*CP*AP*GP*A)-3')


Mass: 7320.728 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.
#4: DNA chain DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*GP*AP*GP*AP*AP*CP*AP*A)-3')


Mass: 7418.804 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.

-
Non-polymers , 3 types, 187 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 0.26M ammonium phosphate monobasic, 35%(v/v) glycerol, pH 7.0, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.55 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.55 Å / Relative weight: 1
ReflectionResolution: 2.19→48.79 Å / Num. all: 50253 / Num. obs: 50179 / % possible obs: 97.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.072 / Rsym value: 0.042 / Net I/σ(I): 8.8
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6950 / Rsym value: 0.287 / % possible all: 93.2

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→35.84 Å / SU ML: 0.37 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 2299 5.11 %RANDOM
Rwork0.1798 ---
obs0.1825 45021 97.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.722 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5997 Å2-0 Å20.3778 Å2
2---1.9848 Å2-0 Å2
3---2.5845 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4846 1956 24 179 7005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077146
X-RAY DIFFRACTIONf_angle_d1.23310095
X-RAY DIFFRACTIONf_dihedral_angle_d22.0062729
X-RAY DIFFRACTIONf_chiral_restr0.0651164
X-RAY DIFFRACTIONf_plane_restr0.004941
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.3022190.21744200X-RAY DIFFRACTION97
2.3822-2.47760.23792420.18854219X-RAY DIFFRACTION97
2.4776-2.59030.23792390.17774225X-RAY DIFFRACTION98
2.5903-2.72680.28152060.18784284X-RAY DIFFRACTION98
2.7268-2.89760.27782370.19494284X-RAY DIFFRACTION98
2.8976-3.12120.22862190.18094291X-RAY DIFFRACTION99
3.1212-3.43510.23292420.15344292X-RAY DIFFRACTION98
3.4351-3.93160.17872310.1514278X-RAY DIFFRACTION98
3.9316-4.95130.19212340.1444325X-RAY DIFFRACTION98
4.9513-35.84390.20092300.17124324X-RAY DIFFRACTION97
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)
10.3410.2852-0.01960.4172-0.07040.0184-0.2184-0.21630.5488-0.03330.7388-0.6591-0.71550.7901-0.42910.5795-0.0280.13540.4202-0.18580.207522.7063-9.3582-17.323
21.8461-0.9876-0.22042.7523-0.11530.0444-0.46050.23360.18870.05720.2274-0.7066-0.0980.0560.05660.22160.02490.03890.2067-0.09380.215331.8062-9.0081.0801
32.70650.1710.52720.16190.13232.7076-0.80980.187-0.3005-0.17290.43050.0342-0.011-0.2620.25780.1938-0.05050.0210.2193-0.07990.159612.312-10.34023.0702
41.95590.11740.87292.1362-1.22761.3611-0.24180.1081-0.6485-0.05210.0651-0.36940.0475-0.22490.17080.324-0.02470.06980.2432-0.11230.219222.2163-14.3085-2.2349
51.2555-1.21910.8532.6582-0.22010.8119-0.16970.18240.5038-0.10390.0631-1.00820.04740.12510.04410.216-0.0250.09410.3697-0.09390.481138.0045-3.7428-0.8426
62.01180.12410.89740.41530.34840.6103-0.0133-1.1945-0.1397-0.08340.39060.31580.09840.2369-0.39480.59060.026-0.2390.4079-0.03070.862353.6763-7.906211.8839
70.9017-0.8489-0.36761.4854-0.32591.0885-0.10230.61460.15930.10630.0576-0.10190.395-0.84420.12650.67250.08060.17560.55170.21640.141911.8110.1186-17.1257
80.3476-0.14780.0821.6301-0.49810.64510.01330.24490.0631-0.23690.08630.1266-0.20180.15680.01610.26340.012-0.00450.20480.04560.03522.33139.84951.1983
99.25890.9264-4.52831.6791-0.87162.3249-0.14481.06361.1074-0.10410.4084-0.0491-0.2893-0.3025-0.07450.1616-0.06320.020.08890.10170.253821.924111.27593.2993
101.5238-0.7205-0.0272.6063-0.23720.7814-0.01160.03960.2671-0.14240.0767-0.3094-0.461-0.3119-0.06680.37530.00850.02250.31890.02110.21412.031415.4394-2.1736
113.2554-1.2293-0.52331.64430.44460.1247-0.02450.499-0.3748-0.3374-0.02260.3134-0.0518-0.12660.00270.2077-0.012-0.06220.3490.00680.097-3.43684.6238-3.0577
129.5666-6.55131.47216.0215-1.15392.6823-0.2357-0.1625-1.59040.74810.13531.15890.07810.2380.42180.22470.04030.24450.10660.07040.2965-11.77876.434311.989
131.27220.2624-0.55460.9657-0.52640.80970.29740.32230.39620.3950.24590.0913-0.3571-0.0681-0.45510.30070.1618-0.05820.34740.14940.38762.145820.05167.0739
142.74310.17210.10131.0969-0.11930.0185-0.456-0.2953-0.26620.61960.3543-0.1418-0.05140.05330.04930.3030.149-0.01540.2459-0.01470.15320.7623-3.912912.1148
155.4635-0.8303-1.35726.35972.19181.3401-0.18761.5441-1.1491.63070.2173-1.58670.7676-0.4019-0.49950.73690.25760.17960.515-0.40060.792935.2121-27.19477.8442
169.1308-2.4693-2.79011.7569-0.23682.01-0.3941.8870.04810.46160.8659-1.2015-0.1381-0.7489-0.59130.37110.33620.08210.8814-0.3080.768535.9161-21.92433.2257
173.2974-1.3546-1.12911.6288-0.0380.6997-0.6317-0.04750.2970.520.5063-0.1257-0.08980.0301-0.02350.33420.1627-0.03370.2358-0.0820.097414.91391.75912.7761
186.05110.99220.88589.54771.41213.22960.07611.01420.60981.28661.61351.4806-0.14560.824-1.52550.55660.0956-0.19330.48940.27190.6722-0.819628.9786.6812
190.8872-0.6047-1.55840.41441.06282.73710.31940.254-0.1269-0.3332-0.41640.1639-0.8462-0.39770.83240.6150.0856-0.07460.431-0.25180.147630.7742-13.4193-59.4723
201.0648-1.1491-0.19361.49140.49230.3060.03540.24-0.1023-0.1688-0.0635-0.18130.1326-0.07530.03790.21320.0018-0.02230.12610.03310.119239.6408-12.6084-41.0818
215.0412-0.89551.30251.76740.27581.3773-0.25880.0021-1.048-0.5170.26770.58680.1768-0.0963-0.02480.2312-0.0348-0.05020.1986-0.04580.373921.8036-14.6391-41.162
222.58370.06461.14972.2192-1.652.06010.2019-0.3174-0.70090.67310.2263-0.162-0.1220.2697-0.42840.36550.0128-0.05170.21280.03630.312826.9803-18.6754-40.9841
232.1296-1.93690.84434.2358-0.18110.45080.16850.47340.3522-0.4352-0.3308-0.77480.02390.34450.11280.12750.04770.05080.32260.0540.166244.1793-8.9915-44.3225
242.57981.2963-2.26461.84431.67169.5526-0.1134-0.65231.36380.3218-0.0655-0.6399-1.22650.55520.28020.36230.092-0.17240.41440.12350.681559.4461-10.3819-29.8407
254.3822-0.52730.68350.0931-0.11860.1543-0.01821.65080.3656-0.4068-0.0612-0.0470.4575-0.13920.0270.55430.1060.0610.51810.13630.068519.83145.2489-59.2568
260.8474-0.6430.4490.5541-0.30130.2388-0.12520.0961-0.0439-0.0460.03070.0222-0.2130.06450.05330.31960.0289-0.04150.19820.03360.076511.20046.2261-40.6415
270.11060.22830.25822.3297-0.26515.7368-0.1087-0.06630.0147-0.4490.1091-0.95510.01681.26950.03830.1891-0.09690.0240.31480.02380.301531.1648.8599-41.7477
281.5326-0.11680.11040.57250.02880.9791-0.15230.02350.56840.1695-0.0499-0.0067-0.1037-0.41750.12510.3717-0.0003-0.00260.2053-0.0030.119921.676312.1607-43.45
291.471-0.765-0.56241.07610.05210.28270.15750.2344-0.3977-0.4425-0.18170.3533-0.05530.0770.02470.25710.0047-0.12170.26950.00910.15844.53771.8334-46.9607
300.54530.1241-0.73351.8813-0.23661.74190.0655-0.0593-0.2990.3931-0.04110.85290.25730.0217-0.0070.30470.0760.16860.29620.11250.3661-2.74512.2482-30.9779
312.1980.72262.11622.1773-1.47715.27220.96641.0059-0.37230.21190.12170.3302-0.12210.49-0.6120.30860.2756-0.10380.50280.2240.37558.156617.629-37.774
322.2709-0.07690.33041.2531-0.01921.0317-0.38930.0978-0.37020.41920.21870.02320.0506-0.04920.10970.25520.10560.01180.19380.06560.152528.2557-7.104-29.6387
336.86083.95143.80264.06791.23825.1658-0.50111.0334-2.36550.75711.5472-1.0366-0.30140.1749-0.42220.60160.25650.37730.4251-0.39140.88842.7269-31.8056-35.052
342.4058-1.80421.31783.2099-1.48181.8203-0.32360.3934-1.10710.73331.06820.7848-0.9345-0.366-0.57750.43150.4494-0.03840.7052-0.14170.675647.5966-25.6568-39.2978
351.0394-0.4944-0.27651.60720.85273.3190.67750.31251.04260.32860.81820.101-0.06810.0657-1.37220.36490.15140.23210.2781-0.04470.751833.8643-22.2852-32.4889
362.6095-1.194-0.26931.0929-0.56550.8692-0.40590.1283-0.00390.41050.27890.0486-0.1554-0.07310.07860.26790.1156-0.03420.18670.01460.103523.2849-1.0701-30.1342
370.4780.50980.18793.5843-2.00992.3712-0.38260.29250.65590.30810.70471.3774-0.2907-0.157-0.33160.46770.1558-0.17360.29880.17010.52146.505721.9425-34.5011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:8)
2X-RAY DIFFRACTION2(chain A and resid 9:44)
3X-RAY DIFFRACTION3(chain A and resid 45:53)
4X-RAY DIFFRACTION4(chain A and resid 54:86)
5X-RAY DIFFRACTION5(chain A and resid 87:148)
6X-RAY DIFFRACTION6(chain A and resid 149:154)
7X-RAY DIFFRACTION7(chain B and resid 2:8)
8X-RAY DIFFRACTION8(chain B and resid 9:44)
9X-RAY DIFFRACTION9(chain B and resid 45:53)
10X-RAY DIFFRACTION10(chain B and resid 54:86)
11X-RAY DIFFRACTION11(chain B and resid 87:139)
12X-RAY DIFFRACTION12(chain B and resid 140:154)
13X-RAY DIFFRACTION13(chain C and resid 501:509)
14X-RAY DIFFRACTION14(chain C and resid 510:519)
15X-RAY DIFFRACTION15(chain C and resid 520:524)
16X-RAY DIFFRACTION16(chain E and resid 601:606)
17X-RAY DIFFRACTION17(chain E and resid 607:620)
18X-RAY DIFFRACTION18(chain E and resid 621:624)
19X-RAY DIFFRACTION19(chain R and resid 2:8)
20X-RAY DIFFRACTION20(chain R and resid 9:43)
21X-RAY DIFFRACTION21(chain R and resid 44:58)
22X-RAY DIFFRACTION22(chain R and resid 59:75)
23X-RAY DIFFRACTION23(chain R and resid 76:145)
24X-RAY DIFFRACTION24(chain R and resid 146:155)
25X-RAY DIFFRACTION25(chain S and resid 2:10)
26X-RAY DIFFRACTION26(chain S and resid 11:49)
27X-RAY DIFFRACTION27(chain S and resid 50:54)
28X-RAY DIFFRACTION28(chain S and resid 55:79)
29X-RAY DIFFRACTION29(chain S and resid 80:138)
30X-RAY DIFFRACTION30(chain S and resid 139:153)
31X-RAY DIFFRACTION31(chain T and resid 501:508)
32X-RAY DIFFRACTION32(chain T and resid 509:520)
33X-RAY DIFFRACTION33(chain T and resid 521:524)
34X-RAY DIFFRACTION34(chain V and resid 601:604)
35X-RAY DIFFRACTION35(chain V and resid 605:608)
36X-RAY DIFFRACTION36(chain V and resid 609:618)
37X-RAY DIFFRACTION37(chain V and resid 619:624)

+
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