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- PDB-5fm8: Structure of the C-terminally extended domain My4 of human myomes... -

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Basic information

Entry
Database: PDB / ID: 5fm8
TitleStructure of the C-terminally extended domain My4 of human myomesin (space group P65)
ComponentsMYOMESIN-1
KeywordsSTRUCTURAL PROTEIN / SARCOMERE / M-BAND / FIBRONECTIN DOMAIN
Function / homology
Function and homology information


extraocular skeletal muscle development / striated muscle myosin thick filament / M band / structural constituent of muscle / protein kinase A signaling / positive regulation of protein secretion / kinase binding / positive regulation of gene expression / protein homodimerization activity / identical protein binding
Similarity search - Function
Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype ...Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Myomesin-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPernigo, S. / Steiner, R.A.
CitationJournal: Structure / Year: 2017
Title: Binding of Myomesin to Obscurin-Like-1 at the Muscle M-Band Provides a Strategy for Isoform-Specific Mechanical Protection.
Authors: Pernigo, S. / Fukuzawa, A. / Beedle, A.E. / Holt, M. / Round, A. / Pandini, A. / Garcia-Manyes, S. / Gautel, M. / Steiner, R.A.
History
DepositionNov 2, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Mar 1, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_symmetry / _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_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYOMESIN-1
B: MYOMESIN-1
C: MYOMESIN-1
D: MYOMESIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9877
Polymers48,7484
Non-polymers2403
Water2,522140
1
A: MYOMESIN-1


Theoretical massNumber of molelcules
Total (without water)12,1871
Polymers12,1871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MYOMESIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2462
Polymers12,1871
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MYOMESIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3683
Polymers12,1871
Non-polymers1812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MYOMESIN-1


Theoretical massNumber of molelcules
Total (without water)12,1871
Polymers12,1871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.410, 97.410, 106.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
MYOMESIN-1 / / 190 KDA CONNECTIN-ASSOCIATED PROTEIN / 190 KDA TITIN-ASSOCIATED PROTEIN / MYOMESIN FAMILY MEMBER 1 / MYOMESIN


Mass: 12186.966 Da / Num. of mol.: 4
Fragment: MY4 EXTENDED AT ITS C-TERMINUS, UNP RESIDUES 510-618
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P52179
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST THREE N-TERMINAL RESIDUES ARE DERIVED FROM THE CLONING STRATEGY

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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: 3.01 Å3/Da / Density % sol: 59.18 % / Description: NONE
Crystal growpH: 8.8
Details: 21 % (W/V) PEG 2000 MME, 10 MM NICL2, 100 MM TRIS/HCL PH 8.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.67
11K, H, -L20.33
ReflectionResolution: 2.05→84.36 Å / Num. obs: 35371 / % possible obs: 99.9 % / Observed criterion σ(I): -1 / Redundancy: 20 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.4
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 20 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.6 / % possible all: 98.7

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
MOLREPphasing
REFMAC5.8.0135refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FM5
Resolution: 2.05→84.36 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.655 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21687 1774 5 %RANDOM
Rwork0.19242 ---
obs0.19364 33912 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.102 Å2
Baniso -1Baniso -2Baniso -3
1-22.92 Å20 Å20 Å2
2--22.92 Å20 Å2
3----45.84 Å2
Refinement stepCycle: LAST / Resolution: 2.05→84.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3084 0 10 140 3234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023235
X-RAY DIFFRACTIONr_bond_other_d0.0080.023081
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.974412
X-RAY DIFFRACTIONr_angle_other_deg1.45737135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0985415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.84123.893131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77215513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2231520
X-RAY DIFFRACTIONr_chiral_restr0.0960.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213649
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02699
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_it1.0742.4121637
X-RAY DIFFRACTIONr_mcbond_other1.0692.4081635
X-RAY DIFFRACTIONr_mcangle_it1.6893.6112041
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9822.4791598
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.053→2.106 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 88 -
Rwork0.268 2495 -
obs--99.08 %
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)
10.44630.16780.48287.3225-5.07264.33190.05130.0853-0.121-0.127-0.2325-0.5110.16760.25130.18120.09080.01970.05390.21610.01320.3984-13.970533.0405-1.4716
21.7767-3.27832.91547.5236-5.07194.85010.170.18460.10770.2131-0.323-0.35850.3970.32190.1530.2315-0.0314-0.0130.2145-0.0410.3486-19.219521.606513.759
31.9784-0.91381.70892.13921.61235.74620.11220.26970.1766-0.54150.0437-0.67030.03620.394-0.15590.5822-0.12740.42960.1166-0.0370.716-10.202136.99-0.941
42.25832.0757-0.86376.5575-0.96591.39830.0938-0.21790.04020.0414-0.16910.14420.0663-0.06260.07520.0493-0.01570.00470.0908-0.0240.302-22.603534.96655.7752
50.3891-0.68690.37031.71620.51633.1837-0.04830.09110.08430.1132-0.0473-0.11640.1710.50430.09560.06760.04460.00010.1773-0.04960.404-21.336827.99629.179
60.8551-0.0681-1.281213.1358-1.03372.35260.1055-0.00750.137-0.152-0.0453-0.0976-0.0590.2482-0.06020.11890.00140.01580.22810.03420.3371-15.737744.16421.0186
70.94811.1033-1.13556.8882-0.33122.7062-0.04810.1066-0.0884-0.6106-0.1799-0.14080.33110.09370.2280.18670.08960.01570.156-0.01830.3486-21.267126.61762.2653
80.7716-0.09620.91996.58644.77285.90140.0688-0.03910.048-0.1824-0.28340.3765-0.305-0.28450.21460.0943-0.02540.04610.16750.0630.3958-30.980658.37916.1408
94.05160.8001-0.80282.2138-1.33542.0052-0.10340.15210.0283-0.26750.08720.3702-0.1307-0.32720.01620.12220.0548-0.02880.0741-0.03490.4372-32.887650.77323.3762
103.80782.4186-0.98648.2262-2.62842.7217-0.07450.432-0.0133-0.2090.1102-0.5170.0087-0.1034-0.03570.1054-0.02120.01690.1357-0.02580.3482-18.670255.49695.029
118.6807-8.3721-1.291110.0275-0.15591.2096-0.0544-0.04480.20330.0750.1549-0.0324-0.0443-0.0793-0.10050.243-0.03260.01290.24680.020.3977-34.147848.980311.0997
122.1994-0.0903-0.09222.1805-1.07010.5467-0.0369-0.0562-0.11350.1529-0.0461-0.0945-0.12290.02760.08310.24890.01770.03090.00790.04480.4134-24.086157.04198.2054
133.30712.4321-0.14818.9599-4.66652.9877-0.19560.4733-0.0923-0.45870.28440.22150.1397-0.0725-0.08880.11320.0262-0.04820.2042-0.07530.3805-29.648845.521-2.5054
141.35541.76290.23146.83170.70971.1858-0.0343-0.03540.017-0.0203-0.25970.2907-0.1322-0.20070.2940.1335-0.0077-0.01770.11480.00930.4064-25.275567.68418.2465
1510.3883-4.0263-3.3135.27740.82266.5444-0.5362-0.4594-0.60850.27550.22470.29870.62560.10590.31160.2606-0.1028-0.03160.2063-0.03590.3419-21.856725.534335.6859
165.30782.0268-3.71272.8571-4.1927.0566-0.13510.084-0.33070.0361-0.05040.04360.33660.14770.18550.2536-0.06360.03470.2467-0.06760.4071-14.283425.240923.9316
173.83464.4240.05485.2815-0.88288.9762-0.0561-0.1617-0.0695-0.146-0.0825-0.02450.01740.030.13850.2584-0.03250.03150.2799-0.01170.3873-32.84925.04536.249
187.21191.192-1.16762.4054-0.10042.4545-0.0730.08270.5651-0.07120.04720.1163-0.1127-0.26380.02580.1614-0.0207-0.00950.21-0.00790.3898-18.054735.876228.4666
190.0698-0.51910.267.32281.02333.5153-0.0188-0.0508-0.0068-0.08730.11390.0763-0.2226-0.3977-0.09510.1959-0.0681-0.06470.3465-0.04140.4676-24.710724.357123.3216
205.16853.2111-3.34592.4214-1.97942.6318-0.09490.38310.44820.07740.11780.21530.2265-0.3008-0.02290.1187-0.0197-0.02750.2226-0.03890.43-13.817633.560426.1475
217.6311-0.6779-4.03151.4843-0.5113.085-0.1301-0.143-0.13470.1192-0.06260.1460.09870.01980.19270.1586-0.0809-0.03670.1242-0.08390.375-14.973229.871730.7963
226.0201-2.9491.63613.1367-1.88224.18-0.5172-0.2630.41710.59480.2195-0.2322-0.32060.05920.29760.3208-0.0517-0.00840.33710.010.4731-24.696459.58637.2133
238.40331.23123.52681.90741.22831.9159-0.24440.01340.3561-0.00970.0618-0.0842-0.26280.04570.18250.2591-0.04890.00370.22050.04990.409-32.44460.182225.6745
245.30560.62312.29162.39020.71132.27540.1633-0.2864-0.34880.1974-0.0138-0.3199-0.04490.3012-0.14960.2266-0.039-0.00690.3050.05560.5021-25.632852.635632.7211
251.5156-3.62172.76428.6604-6.61155.05020.09610.13010.077-0.2003-0.3028-0.24170.16170.27410.20670.281-0.03010.02360.524-0.07260.6195-22.980749.148225.5955
261.7388-4.18142.314810.0893-5.59133.1006-0.2335-0.0950.12610.40420.1484-0.2359-0.2021-0.10530.08510.43810.0224-0.02610.4691-0.01990.6483-22.113861.302524.3509
275.01481.53150.03341.87921.16931.13110.0133-0.0151-0.77040.19810.1409-0.48780.00830.3082-0.15420.1834-0.094-0.00490.31150.0840.578-28.880251.82728.8284
287.39050.83315.74892.14261.21148.2883-0.1495-0.31960.12690.2752-0.1601-0.1774-0.5083-0.17160.30960.21-0.05110.04550.1610.03780.3715-37.415755.951330.9669
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A508 - 519
2X-RAY DIFFRACTION2A520 - 527
3X-RAY DIFFRACTION3A528 - 540
4X-RAY DIFFRACTION4A541 - 564
5X-RAY DIFFRACTION5A565 - 583
6X-RAY DIFFRACTION6A584 - 590
7X-RAY DIFFRACTION7A591 - 608
8X-RAY DIFFRACTION8B508 - 526
9X-RAY DIFFRACTION9B527 - 550
10X-RAY DIFFRACTION10B551 - 560
11X-RAY DIFFRACTION11B561 - 568
12X-RAY DIFFRACTION12B569 - 588
13X-RAY DIFFRACTION13B589 - 597
14X-RAY DIFFRACTION14B598 - 608
15X-RAY DIFFRACTION15C508 - 517
16X-RAY DIFFRACTION16C518 - 534
17X-RAY DIFFRACTION17C535 - 541
18X-RAY DIFFRACTION18C542 - 563
19X-RAY DIFFRACTION19C564 - 568
20X-RAY DIFFRACTION20C569 - 588
21X-RAY DIFFRACTION21C589 - 608
22X-RAY DIFFRACTION22D508 - 517
23X-RAY DIFFRACTION23D518 - 534
24X-RAY DIFFRACTION24D535 - 556
25X-RAY DIFFRACTION25D557 - 563
26X-RAY DIFFRACTION26D564 - 568
27X-RAY DIFFRACTION27D569 - 593
28X-RAY DIFFRACTION28D594 - 608

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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

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