[English] 日本語
Yorodumi
- PDB-2ydx: Crystal structure of human S-adenosylmethionine synthetase 2, bet... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ydx
TitleCrystal structure of human S-adenosylmethionine synthetase 2, beta subunit
ComponentsMETHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA
KeywordsOXIDOREDUCTASE / TRANSFERASE
Function / homology
Function and homology information


methionine adenosyltransferase regulator activity / dTDP-4-dehydrorhamnose reductase activity / methionine adenosyltransferase complex / dTDP-rhamnose biosynthetic process / Methylation / S-adenosylmethionine biosynthetic process / extracellular polysaccharide biosynthetic process / one-carbon metabolic process / Ub-specific processing proteases / enzyme binding ...methionine adenosyltransferase regulator activity / dTDP-4-dehydrorhamnose reductase activity / methionine adenosyltransferase complex / dTDP-rhamnose biosynthetic process / Methylation / S-adenosylmethionine biosynthetic process / extracellular polysaccharide biosynthetic process / one-carbon metabolic process / Ub-specific processing proteases / enzyme binding / extracellular exosome / nucleus / cytosol
Similarity search - Function
dTDP-4-dehydrorhamnose reductase family / RmlD-like substrate binding domain / RmlD substrate binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / RESVERATROL / Chem-TXP / Methionine adenosyltransferase 2 subunit beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.8 Å
AuthorsMuniz, J.R.C. / Shafqat, N. / Pike, A.C.W. / Yue, W.W. / Vollmar, M. / Papagriogriou, V. / Roos, A. / Gileadi, O. / von Delft, F. / Kavanagh, K.L. ...Muniz, J.R.C. / Shafqat, N. / Pike, A.C.W. / Yue, W.W. / Vollmar, M. / Papagriogriou, V. / Roos, A. / Gileadi, O. / von Delft, F. / Kavanagh, K.L. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Oppermann, U.
CitationJournal: Biochem.J. / Year: 2013
Title: Insight Into S-Adenosylmethionine Biosynthesis from the Crystal Structures of the Human Methionine Adenosyltransferase Catalytic and Regulatory Subunits.
Authors: Shafqat, N. / Muniz, J.R.C. / Pilka, E.S. / Papagrigoriou, E. / von Delft, F. / Oppermann, U. / Yue, W.W.
History
DepositionMar 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references / Structure summary / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_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.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_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_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_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: METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA
B: METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA
C: METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA
D: METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA
E: METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,60140
Polymers177,7325
Non-polymers7,86935
Water9,422523
1
B: METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA
hetero molecules

B: METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,45318
Polymers71,0932
Non-polymers3,36016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
Buried area9430 Å2
ΔGint-135.8 kcal/mol
Surface area25030 Å2
MethodPISA
2
A: METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA
C: METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,20516
Polymers71,0932
Non-polymers3,11214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-110 kcal/mol
Surface area25050 Å2
MethodPISA
3
D: METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA
E: METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,16915
Polymers71,0932
Non-polymers3,07613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-93.4 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.389, 163.389, 252.882
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

-
Components

-
Protein , 1 types, 5 molecules ABCDE

#1: Protein
METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA / DTDP-4-KETO-6-DEOXY-D-GLUCOSE 4-REDUCTASE / METHIONINE ADENOSYLTRANSFERASE II BETA / MAT II BETA / ...DTDP-4-KETO-6-DEOXY-D-GLUCOSE 4-REDUCTASE / METHIONINE ADENOSYLTRANSFERASE II BETA / MAT II BETA / S-ADENOSYLMETHIONINE SYNTHETASE 2 / MAT2B


Mass: 35546.371 Da / Num. of mol.: 5 / Fragment: RESIDUES 28-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q9NZL9

-
Non-polymers , 6 types, 558 molecules

#2: Chemical
ChemComp-STL / RESVERATROL


Mass: 228.243 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C14H12O3
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-TXP / 1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE


Mass: 747.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H32N7O17P3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 4.75 Å3/Da / Density % sol: 74.09 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97926
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.8→58.96 Å / Num. obs: 78936 / % possible obs: 93.2 % / Observed criterion σ(I): 1.1 / Redundancy: 6.9 % / Biso Wilson estimate: 73.24 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 1.1 / % possible all: 56

-
Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.8→58.96 Å / Cor.coef. Fo:Fc: 0.9376 / Cor.coef. Fo:Fc free: 0.9306 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=STL NAP SO4 CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=12675. NUMBER WITH APPROX DEFAULT CCP4 ATOM ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=STL NAP SO4 CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=12675. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=505. NUMBER TREATED BY BAD NON- BONDED CONTACTS=1.
RfactorNum. reflection% reflectionSelection details
Rfree0.1882 3936 4.99 %RANDOM
Rwork0.1675 ---
obs0.1686 78848 --
Displacement parametersBiso mean: 64.44 Å2
Baniso -1Baniso -2Baniso -3
1--4.9622 Å20 Å20 Å2
2---4.9622 Å20 Å2
3---9.9244 Å2
Refine analyzeLuzzati coordinate error obs: 0.382 Å
Refinement stepCycle: LAST / Resolution: 2.8→58.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12090 0 506 523 13119
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112966HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0917694HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5691SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes401HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1904HARMONIC5
X-RAY DIFFRACTIONt_it12966HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion3.07
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1669SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14774SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2394 140 5.74 %
Rwork0.2505 2297 -
all0.2498 2437 -
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)
11.57430.9323-0.95381.3008-0.93762.5861-0.04560.51370.1906-0.48510.1069-0.1248-0.13980.4647-0.0613-0.304-0.1311-0.01930.3040.0575-0.2224-11.7302-73.4411-13.1809
21.6868-2.3619-2.15421.131-0.85330.0661-0.0296-0.06730.163-0.0012-0.01320.1239-0.09880.02730.0428-0.0831-0.05540.15150.20340.06730.1069-25.0505-59.1401-2.7052
30.7682-0.08511.66371.74590.42241.366-0.02140.3150.1478-0.42440.03120.482-0.2986-0.0168-0.0098-0.2408-0.022-0.06930.19540.1235-0.1193-28.4635-71.7604-12.3305
40-0.99081.028601.46960.9757-0.02290.06670.0629-0.04550.00980.05890.0644-0.00570.0131-0.18080.0939-0.1520.27350.04540.0377-40.7882-79.5215-11.1265
52.65350.1543-0.35161.0091-0.14741.0622-0.05090.0330.2896-0.06950.08640.2231-0.1447-0.0816-0.0355-0.2611-0.0365-0.02890.18550.0492-0.0296-27.6797-76.76562.2556
61.0143-0.97160.60580.1835-0.16340.0066-0.00620.0576-0.0402-0.01930.02250.0155-0.14650.019-0.0162-0.3021-0.05370.02660.28160.070.219-38.7765-71.96084.6542
70.8259-0.23930.91450.01020.04070.5644-0.0388-0.0921-0.07850.11610.01350.10040.13970.22560.0252-0.304-0.0385-0.02890.3040.0116-0.1442-23.6441-85.25692.7999
82.3618-1.62130.66430.2313-1.54764.56450.01840.01940.06260.2360.02890.1297-0.03380.1076-0.0473-0.268-0.10140.00410.304-0.0972-0.0962-11.9577-71.043927.7681
94.3947-0.92290.51433.8440.09512.1525-0.0404-0.5349-0.5442-0.18080.04470.01330.34540.3417-0.0043-0.28530.0771-0.0030.05390.10740.1132-64.7466-89.129212.8379
102.28982.18220.16760.09290.85222.24020.0142-0.0838-0.00320.0649-0.06320.0361-0.11640.04970.049-0.2150.1124-0.0560.3027-0.14620.0423-68.2612-77.912431.3634
113.6248-0.4305-0.59560-0.0140.4156-0.0762-0.54420.13780.4160.0549-0.44710.08160.22380.0214-0.3040.0844-0.06620.304-0.0927-0.0998-54.6872-76.343724.0281
125.8977-0.86160.07472.31120.40021.188-0.1724-0.54420.5442-0.0310.01670.1404-0.28530.13480.1557-0.28230.0085-0.03410.0814-0.11350.1067-63.4603-69.942414.5426
130.89342.6001-1.40636.10782.91041.49510.0143-0.52570.54420.2230.17460.3955-0.24990.0275-0.189-0.3040.1033-0.0201-0.3035-0.1520.304-71.7561-54.956418.3553
142.108-1.4276-1.314300.61182.36940.0214-0.16850.5442-0.0830.1519-0.0795-0.32560.2406-0.1733-0.304-0.0311-0.0114-0.1673-0.06090.2581-64.5188-65.61069.5112
152.7823-0.727-1.23080.39362.50770.003-0.0018-0.0848-0.04840.171-0.00390.1209-0.187-0.01550.0056-0.2876-0.0551-0.0504-0.0235-0.1520.304-94.187-60.904715.0422
164.762301.84481.4631-0.15085.44960.0437-0.5418-0.22180.31160.0074-0.22660.32880.128-0.051-0.2236-0.0258-0.03610.21990.051-0.1053-0.4064-95.628121.951
171.58390.47451.93785.117-1.24180.16180.0409-0.2482-0.5442-0.07620.0297-0.22890.34980.0603-0.0706-0.08590.049-0.04310.14790.152-0.07-1.5411-109.79720.2229
181.5318-0.0112-2.46133.5193-0.2752.2571-0.0539-0.373-0.54420.0620.11550.15460.4374-0.0345-0.06160.0567-0.1108-0.0537-0.05360.1520.0856-13.6178-116.23117.9584
192.320.71970.1011.4620.55375.7256-0.0960.298-0.5386-0.10410.07280.08490.5424-0.32110.0232-0.2678-0.0845-0.04650.0997-0.0229-0.1109-13.7428-103.9843.5078
200.52021.30071.43222.80151.88751.80740.05410.0784-0.3848-0.13160.17050.18780.2971-0.096-0.2246-0.0559-0.152-0.01880.13130.00270.0746-17.7544-115.5836.4116
214.5081.71820.78270.90761.05080.76560.05390.0133-0.1464-0.0394-0.11790.166-0.0064-0.04260.064-0.2918-0.1184-0.03950.18530.0604-0.1479-20.549-97.42558.4847
226.184-2.03162.50584.5812.37960.89950.017-0.06750.0133-0.11270.0017-0.1727-0.05570.1066-0.0187-0.3029-0.10080.01160.304-0.028-0.2796-6.0194-92.7809-8.7613
2302.0276-1.24550.21251.91950.22980.03280.0805-0.1497-0.08860.00060.02710.12190.0805-0.0334-0.304-0.152-0.05960.304-0.0592-0.17872.332-99.5486-19.6946
242.819-0.48550.04931.5383-1.20526.805-0.215-0.46550.0190.12390.209-0.11110.54420.18990.0060.0130.02750.02320.23890.0509-0.304-10.5843-91.497-41.4763
252.7616-0.12371.17261.9754-0.59081.0485-0.16850.1192-0.54420.15040.1020.38620.5442-0.51150.06650.0204-0.1520.1520.3040.023-0.304-27.873-98.8521-44.8498
262.488-0.19930.32651.24410.57743.9486-0.21230.305-0.2392-0.1531-0.05180.39060.3685-0.54420.2641-0.1632-0.1081-0.00730.3040.0192-0.304-26.8635-87.6084-58.097
270-2.8753-0.421400.20780.70570.010.1822-0.1042-0.1198-0.02750.0248-0.0240.05650.01750.0529-0.12180.02430.1577-0.0754-0.2335-10.811-91.2465-78.526
281.8382-0.7318-0.53650-0.60096.4351-0.02720.35370.1612-0.24990.032-0.062-0.39560.4054-0.00470.17190.01820.0078-0.02320.0231-0.2497-2.4255-68.056-76.6497
296.3742.1523-0.99286.026-0.13180-0.04810.07340.5390.03790.1666-0.1432-0.18180.082-0.11850.30350.0363-0.0832-0.29260.0999-0.2838-5.3585-54.1342-74.932
300.0067-1.85361.48823.1177-1.09342.1691-0.0502-0.01890.214-0.13510.1341-0.0711-0.189-0.3522-0.08390.3040.152-0.0985-0.3040.0381-0.3029-19.0864-48.7227-70.3593
312.6985-0.59110.57361.1098-0.89473.338-0.0611-0.25870.5-0.17450.10550.1411-0.30170.1367-0.04440.3030.152-0.007-0.0836-0.0484-0.301-11.4087-60.0182-62.7523
322.3076-1.3515-0.24920.62990.90584.8068-0.1879-0.52290.35650.14760.14530.068-0.5442-0.54420.04260.19070.1520.04870.0915-0.014-0.2945-18.8175-59.8544-58.003
3300.44521.68370.66470.69625.88620.0928-0.09880.23820.0565-0.11750.2367-0.3476-0.33630.0246-0.00990.152-0.00550.25660.0922-0.3037-17.823-66.5539-57.7815
340.0112-0.7780.856600.04350.16260-0.04170.10370.03450.00570.0204-0.00060.033-0.00570.0610.11270.02740.1824-0.1512-0.1548-0.6748-63.0066-34.8271
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 27:95
2X-RAY DIFFRACTION2CHAIN A AND RESID 96:111
3X-RAY DIFFRACTION3CHAIN A AND RESID 112:147
4X-RAY DIFFRACTION4CHAIN A AND RESID 148:152
5X-RAY DIFFRACTION5CHAIN A AND RESID 153:287
6X-RAY DIFFRACTION6CHAIN A AND RESID 288:292
7X-RAY DIFFRACTION7CHAIN A AND RESID 293:324
8X-RAY DIFFRACTION8CHAIN A AND RESID 325:338
9X-RAY DIFFRACTION9CHAIN B AND RESID 27:95
10X-RAY DIFFRACTION10CHAIN B AND RESID 96:111
11X-RAY DIFFRACTION11CHAIN B AND RESID 112:171
12X-RAY DIFFRACTION12CHAIN B AND RESID 172:253
13X-RAY DIFFRACTION13CHAIN B AND RESID 254:289
14X-RAY DIFFRACTION14CHAIN B AND RESID 290:325
15X-RAY DIFFRACTION15CHAIN B AND RESID 326:338
16X-RAY DIFFRACTION16CHAIN C AND RESID 27:91
17X-RAY DIFFRACTION17CHAIN C AND RESID 92:135
18X-RAY DIFFRACTION18CHAIN C AND RESID 136:176
19X-RAY DIFFRACTION19CHAIN C AND RESID 177:279
20X-RAY DIFFRACTION20CHAIN C AND RESID 280:301
21X-RAY DIFFRACTION21CHAIN C AND RESID 302:315
22X-RAY DIFFRACTION22CHAIN C AND RESID 316:327
23X-RAY DIFFRACTION23CHAIN C AND RESID 328:338
24X-RAY DIFFRACTION25CHAIN D AND RESID 96:172
25X-RAY DIFFRACTION26CHAIN D AND RESID 173:318
26X-RAY DIFFRACTION27CHAIN D AND RESID 319:338
27X-RAY DIFFRACTION28CHAIN E AND RESID 27:91
28X-RAY DIFFRACTION29CHAIN E AND RESID 92:135
29X-RAY DIFFRACTION30CHAIN E AND RESID 136:170
30X-RAY DIFFRACTION31CHAIN E AND RESID 171:204
31X-RAY DIFFRACTION32CHAIN E AND RESID 205:290
32X-RAY DIFFRACTION33CHAIN E AND RESID 291:328
33X-RAY DIFFRACTION34CHAIN E AND RESID 329:337

+
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