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- PDB-6mw7: Crystal structure of ATPase module of SMCHD1 bound to ATP -

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Basic information

Entry
Database: PDB / ID: 6mw7
TitleCrystal structure of ATPase module of SMCHD1 bound to ATP
ComponentsStructural maintenance of chromosomes flexible hinge domain-containing protein 1
KeywordsHYDROLASE / GHKL-ATPase / epigenetic repressor / Bosma arhinia microphthalmia / fascioscapulohumeral muscular dystrophy type 2
Function / homology
Function and homology information


: / : / : / nose development / Barr body / dosage compensation by inactivation of X chromosome / positive regulation of double-strand break repair via nonhomologous end joining / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / negative regulation of double-strand break repair via homologous recombination / positive regulation of DNA repair ...: / : / : / nose development / Barr body / dosage compensation by inactivation of X chromosome / positive regulation of double-strand break repair via nonhomologous end joining / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / negative regulation of double-strand break repair via homologous recombination / positive regulation of DNA repair / double-strand break repair / site of double-strand break / protein homodimerization activity / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Structural maintenance of chromosomes flexible hinge domain-containing protein 1 / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Structural maintenance of chromosomes flexible hinge domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.194 Å
AuthorsPedersen, L.C. / Inoue, K. / Kim, S. / Perera, L. / Shaw, N.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) United States
CitationJournal: Commun Biol / Year: 2019
Title: A ubiquitin-like domain is required for stabilizing the N-terminal ATPase module of human SMCHD1.
Authors: Pedersen, L.C. / Inoue, K. / Kim, S. / Perera, L. / Shaw, N.D.
History
DepositionOct 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Structural maintenance of chromosomes flexible hinge domain-containing protein 1
B: Structural maintenance of chromosomes flexible hinge domain-containing protein 1
C: Structural maintenance of chromosomes flexible hinge domain-containing protein 1
D: Structural maintenance of chromosomes flexible hinge domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,23114
Polymers260,9864
Non-polymers2,24510
Water16,700927
1
A: Structural maintenance of chromosomes flexible hinge domain-containing protein 1
B: Structural maintenance of chromosomes flexible hinge domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,5566
Polymers130,4932
Non-polymers1,0634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-50 kcal/mol
Surface area43880 Å2
MethodPISA
2
C: Structural maintenance of chromosomes flexible hinge domain-containing protein 1
D: Structural maintenance of chromosomes flexible hinge domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,6758
Polymers130,4932
Non-polymers1,1826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-79 kcal/mol
Surface area43880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.756, 148.012, 191.138
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Structural maintenance of chromosomes flexible hinge domain-containing protein 1 / SMC hinge domain-containing protein 1


Mass: 65246.504 Da / Num. of mol.: 4 / Fragment: residues 24-580 / Mutation: E147A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMCHD1, KIAA0650 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2(DE3)
References: UniProt: A6NHR9, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Non-polymers , 5 types, 937 molecules

#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 927 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25 mM Bis Tris Propane pH 6.8, 50mM Ammonium sulfate, 5% glycerol, 7.5% PEG 8000, 5mM DTT

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 153427 / % possible obs: 97.4 % / Redundancy: 9.1 % / Rpim(I) all: 0.039 / Rsym value: 0.12 / Net I/σ(I): 4.1
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6560 / CC1/2: 0.841 / Rpim(I) all: 0.287 / Rsym value: 0.799 / % possible all: 84.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.194→47.785 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2301 7708 5.04 %random selection
Rwork0.1965 ---
obs0.1982 152943 96.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.194→47.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16207 0 134 927 17268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416735
X-RAY DIFFRACTIONf_angle_d0.66422706
X-RAY DIFFRACTIONf_dihedral_angle_d15.0446098
X-RAY DIFFRACTIONf_chiral_restr0.0482486
X-RAY DIFFRACTIONf_plane_restr0.0042919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.194-2.2190.35412290.33083780X-RAY DIFFRACTION77
2.219-2.24510.38112100.32234372X-RAY DIFFRACTION88
2.2451-2.27240.35812490.30384411X-RAY DIFFRACTION90
2.2724-2.30120.31462420.29354597X-RAY DIFFRACTION93
2.3012-2.33150.28862640.28564682X-RAY DIFFRACTION95
2.3315-2.36340.3042390.28694801X-RAY DIFFRACTION96
2.3634-2.39720.30332620.27224854X-RAY DIFFRACTION99
2.3972-2.4330.29282740.26824909X-RAY DIFFRACTION99
2.433-2.4710.29462400.25754857X-RAY DIFFRACTION97
2.471-2.51150.29382510.25594671X-RAY DIFFRACTION95
2.5115-2.55480.28232740.23954921X-RAY DIFFRACTION99
2.5548-2.60120.24132390.2364966X-RAY DIFFRACTION100
2.6012-2.65130.26732590.23334972X-RAY DIFFRACTION100
2.6513-2.70540.24782420.2294944X-RAY DIFFRACTION100
2.7054-2.76420.24653060.22454889X-RAY DIFFRACTION100
2.7642-2.82850.25282590.2184981X-RAY DIFFRACTION100
2.8285-2.89920.23272720.21284944X-RAY DIFFRACTION100
2.8992-2.97760.25372570.2114983X-RAY DIFFRACTION100
2.9776-3.06520.23592610.1984972X-RAY DIFFRACTION100
3.0652-3.16410.23942700.20774934X-RAY DIFFRACTION100
3.1641-3.27720.24552410.20485018X-RAY DIFFRACTION100
3.2772-3.40840.23852580.19684981X-RAY DIFFRACTION100
3.4084-3.56340.18582770.17934918X-RAY DIFFRACTION99
3.5634-3.75120.19042210.17044699X-RAY DIFFRACTION93
3.7512-3.98620.20532510.16365021X-RAY DIFFRACTION100
3.9862-4.29380.17132550.14885026X-RAY DIFFRACTION100
4.2938-4.72550.16312580.14165086X-RAY DIFFRACTION100
4.7255-5.40850.19672810.15265053X-RAY DIFFRACTION100
5.4085-6.8110.25272770.18555067X-RAY DIFFRACTION99
6.811-47.79580.23142900.18524926X-RAY DIFFRACTION93
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.83230.94552.07243.11980.13977.6373-0.29760.9381-0.1074-0.41950.29050.07070.36650.248-0.02060.7505-0.0515-0.06690.64870.00860.402422.106651.98144.3088
25.28622.6325.94671.31962.96746.6944-0.77361.0177-0.1257-1.90080.90961.3585-0.9992-0.5436-0.10181.0923-0.2256-0.30551.14350.09090.646417.651242.427235.4664
37.25982.1391.88592.42611.88795.76780.0920.2137-0.2255-0.47790.01230.53341.0207-0.7947-0.09440.8225-0.1627-0.06410.5923-0.03570.461215.715848.623250.8541
40.3850.65750.71743.45491.77661.834-0.0188-0.02260.0035-0.1144-0.05790.30550.0517-0.18770.0680.36460.0042-0.03410.30490.03850.370625.883575.425181.2431
55.1071-0.47980.94743.0215-0.15622.89830.130.20640.6105-0.0864-0.053-0.0654-0.6266-0.1001-0.0120.5504-0.02080.06290.2790.0120.377728.137796.359183.7331
61.1647-0.2663-1.05318.56151.64613.04780.0519-0.0704-0.0033-0.54380.1623-0.5381-0.15050.5688-0.16180.34420.00210.00750.3627-0.0010.351439.131681.302476.3043
70.3818-0.1230.27561.45070.08812.28480.07480.05070.143-0.4615-0.05520.1262-0.3342-0.1079-0.00180.48120.0251-0.02440.32740.02330.411827.436688.88575.6108
80.6212-0.2461.11611.8479-1.58692.5423-0.0735-0.2960.110.22630.13670.0469-0.3816-0.232-0.05010.3538-0.02120.00980.3973-0.04180.379533.802387.1634104.4597
91.838-0.37181.38952.0546-0.38873.98010.0601-0.2326-0.14830.19140.0214-0.07690.2927-0.0885-0.05670.2546-0.0119-0.01370.34060.0290.344737.788571.5814105.8041
103.894-2.0442-2.0522.80231.79582.1157-0.1041-0.5189-0.05470.210.0418-0.0335-0.01770.26050.06820.43310.0056-0.02880.61910.01820.356144.098277.8518122.4274
113.60352.6199-1.21174.0473-0.36733.8035-0.0740.5972-0.0367-1.05890.1745-0.3872-0.68710.5839-0.08480.9968-0.05020.11380.59160.00160.485840.757789.299552.9868
123.24882.5507-1.53014.1033-0.48113.11990.0738-0.22040.07920.1489-0.10820.2020.10490.01120.03770.37720.0755-0.03270.27690.01430.379223.262456.868684.5821
131.67060.4886-0.22773.6768-0.28982.44290.07090.1258-0.1089-0.3113-0.05040.13510.2527-0.0161-0.04340.4116-0.0004-0.040.2739-0.02780.296723.184451.206576.2536
145.01950.9984-2.87272.7556-1.15494.41190.15790.41560.236-0.21230.02050.54970.0174-0.652-0.18230.3977-0.046-0.07570.317-0.0270.384315.875459.254582.5388
154.97242.48730.32864.2463-0.02332.4032-0.04550.2136-0.0806-0.43270.1013-0.08690.270.0185-0.03920.66450.03410.01030.311-0.00990.327729.282253.316665.89
169.3745-0.22810.18482.55441.44643.6418-0.2858-0.1137-0.3757-0.49090.1021-0.06960.38420.12730.18090.76190.03180.04040.33520.00950.43829.719938.228570.7366
173.4249-0.4167-1.49462.53970.24764.32230.057-0.34110.04560.2936-0.07140.05350.26620.09380.02320.4313-0.0239-0.0120.22550.0120.355823.044448.646391.1364
181.558-0.7096-2.05792.24221.63412.9895-0.0689-0.14570.05170.4766-0.00230.27840.3955-0.03620.10210.5486-0.06740.03830.40150.00550.480514.476950.9896103.044
191.45950.0236-1.03172.1837-0.57285.75910.1134-0.16460.15870.4669-0.02170.5454-0.4779-0.4412-0.05640.4639-0.0070.08160.4345-0.04490.57219.964166.1155102.5524
202.7867-0.60412.93341.7403-0.51243.0630.1467-0.40560.33060.08420.15270.88190.0049-1.0567-0.27110.8421-0.02240.31270.8434-0.01510.8491-1.320360.5995115.5694
216.21520.5661-1.58293.02930.74545.1262-0.14960.80390.1609-0.3430.1912-0.1676-0.41350.3833-0.0560.8125-0.13480.07240.65010.02830.4221-19.237197.592679.7424
222.1364-1.79151.25177.7261-6.00744.541-0.05780.3460.096-0.2633-0.2215-0.4806-0.18420.17430.11210.484-0.02020.030.3068-0.030.318-25.640184.855498.9131
236.98315.05970.66855.77180.61460.79220.0635-0.06650.17660.0253-0.0864-0.23780.06740.0238-0.01130.42250.0548-0.03340.3256-0.0080.3767-28.850667.0761122.2954
249.8172-0.9652-1.79653.42920.69023.2460.15720.1925-1.071-0.3146-0.1203-0.06880.25330.05890.00060.4582-0.03-0.07830.2786-0.00360.4557-30.70851.0787116.8533
254.76143.09590.02432.036-0.36225.5032-0.1883-0.1252-0.1717-0.5370.16920.1139-0.2503-0.60130.07650.4080.0202-0.00490.2206-0.04840.3111-36.126757.5936110.1808
260.9956-0.36970.07690.6413-0.07223.03690.0998-0.0107-0.0825-0.18670.00260.13550.0767-0.4173-0.06090.3886-0.0355-0.03950.35010.01130.3911-39.32467.0653112.4044
270.9401-0.01290.16373.70850.01591.2926-0.06720.0498-0.269-0.53880.0626-0.21080.32140.11660.02250.67680.03490.03180.3773-0.0540.4348-28.033156.35100.4861
282.6304-0.9094-0.74742.03350.52295.50850.0886-0.2984-0.12850.11070.0316-0.20830.12950.1013-0.11420.3492-0.0486-0.06340.22980.02790.4089-29.408258.1699125.8062
290.6307-0.08390.03912.61910.35352.76080.012-0.3934-0.14410.26780.1065-0.0165-0.0569-0.1105-0.09730.3177-0.0453-0.0570.46840.06960.3674-35.185163.275138.3164
301.1884-0.13350.63441.54-0.88864.5096-0.0415-0.52820.09860.55480.13960.2107-0.6147-0.7654-0.08780.57950.08770.01620.6446-0.02110.4064-41.453175.2054144.566
313.93540.21560.02443.2995-0.51122.9215-0.03710.61660.007-0.99850.08090.15570.3845-0.4426-0.03841.0298-0.0548-0.14770.7153-0.03920.5165-45.644257.630382.4194
321.6521.12840.97855.93173.77484.4520.08920.0586-0.1143-0.2358-0.0350.06280.1422-0.2894-0.0410.5446-0.0229-0.03030.33580.05480.3604-37.886668.9186101.6709
336.8629-0.9276-0.3153.52290.01152.56990.12550.20650.24830.1071-0.0757-0.1491-0.25070.0048-0.05020.4242-0.002-0.00720.2457-0.02030.2875-24.2508100.8655116.1632
341.01080.39790.85011.5691-0.02862.64270.00520.1669-0.0458-0.29960.0352-0.1702-0.09420.1908-0.01580.4608-0.00390.03380.2949-0.00990.3702-23.789791.7086105.1808
356.9243-1.1803-0.35683.1367-0.8462.6312-0.306-0.06890.1411-0.21070.1097-0.1121-0.1678-0.19160.14040.76180.0072-0.05970.36780.02260.4931-31.0768109.5511102.9189
363.1867-0.77511.07872.1162-0.29582.87020.0534-0.29870.0740.3226-0.0371-0.1525-0.2003-0.0967-0.01170.51020.0002-0.00150.2349-0.00920.3742-24.231399.4132123.7865
371.2084-0.70031.11941.8613-1.41961.4807-0.248-0.2510.03520.60840.1544-0.3552-0.3242-0.0720.11520.75830.0079-0.14890.4001-0.0460.5113-15.666896.8351135.2606
381.7113-0.42140.77272.9944-0.13913.8511-0.1289-0.2395-0.06980.63940.0991-0.54090.05770.29970.00810.50010.0335-0.11540.38260.00850.5106-10.825381.9564135.1424
394.1474-4.9732-3.17429.1956-1.45642.00090.1199-3.18420.64521.92180.1283-2.30050.33492.5231-0.07040.76180.1025-0.3941.22360.04951.2135.046878.386142.2782
404.735-0.3824-1.64195.31241.39255.442-0.3812-0.52410.11411.26740.228-0.996-0.35311.0820.14191.05220.0679-0.45150.6951-0.07130.8056-1.79388.8642150.6899
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 25:65)
2X-RAY DIFFRACTION2(chain A and resid 66:69)
3X-RAY DIFFRACTION3(chain A and resid 70:111)
4X-RAY DIFFRACTION4(chain A and resid 112:157)
5X-RAY DIFFRACTION5(chain A and resid 158:181)
6X-RAY DIFFRACTION6(chain A and resid 182:221)
7X-RAY DIFFRACTION7(chain A and resid 222:339)
8X-RAY DIFFRACTION8(chain A and resid 340:465)
9X-RAY DIFFRACTION9(chain A and resid 466:547)
10X-RAY DIFFRACTION10(chain A and resid 548:578)
11X-RAY DIFFRACTION11(chain B and resid 26:119)
12X-RAY DIFFRACTION12(chain B and resid 120:164)
13X-RAY DIFFRACTION13(chain B and resid 165:206)
14X-RAY DIFFRACTION14(chain B and resid 207:249)
15X-RAY DIFFRACTION15(chain B and resid 250:291)
16X-RAY DIFFRACTION16(chain B and resid 292:316)
17X-RAY DIFFRACTION17(chain B and resid 317:372)
18X-RAY DIFFRACTION18(chain B and resid 373:464)
19X-RAY DIFFRACTION19(chain B and (resid 465:495 or resid 499:548))
20X-RAY DIFFRACTION20(chain B and resid 549:574)
21X-RAY DIFFRACTION21(chain C and resid 25:107)
22X-RAY DIFFRACTION22(chain C and resid 108:128)
23X-RAY DIFFRACTION23(chain C and resid 129:157)
24X-RAY DIFFRACTION24(chain C and resid 158:177)
25X-RAY DIFFRACTION25(chain C and resid 178:192)
26X-RAY DIFFRACTION26(chain C and resid 193:257)
27X-RAY DIFFRACTION27(chain C and resid 258:316)
28X-RAY DIFFRACTION28(chain C and resid 317:372)
29X-RAY DIFFRACTION29(chain C and resid 373:480)
30X-RAY DIFFRACTION30(chain C and resid 481:577)
31X-RAY DIFFRACTION31(chain D and resid 26:87)
32X-RAY DIFFRACTION32(chain D and resid 88:138)
33X-RAY DIFFRACTION33(chain D and resid 139:181)
34X-RAY DIFFRACTION34(chain D and resid 182:290)
35X-RAY DIFFRACTION35(chain D and resid 291:316)
36X-RAY DIFFRACTION36(chain D and resid 317:372)
37X-RAY DIFFRACTION37(chain D and resid 373:446)
38X-RAY DIFFRACTION38(chain D and resid 463:551)
39X-RAY DIFFRACTION39(chain D and resid 552:555)
40X-RAY DIFFRACTION40(chain D and resid 556:572)

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