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- PDB-5nbl: Crystal structure of the Arp4-N-actin(APO-state) heterodimer boun... -

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Basic information

Entry
Database: PDB / ID: 5nbl
TitleCrystal structure of the Arp4-N-actin(APO-state) heterodimer bound by a nanobody
Components
  • Actin-related protein 4
  • Actin
  • Unknown peptide
  • nAct-Nanobody
KeywordsHYDROLASE / Nuclear actin / Actin-related-proteins / Chromatin remodeling / Nanobody / INO80 / SWR1 / NuA4
Function / homology
Function and homology information


mitotic actomyosin contractile ring contraction / RHOA GTPase cycle / cellular bud neck contractile ring / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / ascospore wall assembly / vacuole inheritance / actin cortical patch / Swr1 complex ...mitotic actomyosin contractile ring contraction / RHOA GTPase cycle / cellular bud neck contractile ring / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / ascospore wall assembly / vacuole inheritance / actin cortical patch / Swr1 complex / Platelet degranulation / : / Ino80 complex / kinetochore assembly / SWI/SNF complex / NuA4 histone acetyltransferase complex / establishment of cell polarity / actin filament bundle / protein secretion / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / endocytosis / chromatin organization / histone binding / hydrolase activity / chromatin remodeling / DNA repair / DNA-templated transcription / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP binding / identical protein binding / nucleus
Similarity search - Function
ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family ...ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Actin / Actin-related protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Vicugna pacos (alpaca)
Trichoplusia ni (cabbage looper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsKnoll, K.R. / Eustermann, S. / Hopfner, K.P.
Funding support3items
OrganizationGrant numberCountry
German Research FoundationGRK1721
German Research FoundationCRC1064
European Research CouncilATMMACHINE
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: The nuclear actin-containing Arp8 module is a linker DNA sensor driving INO80 chromatin remodeling.
Authors: Knoll, K.R. / Eustermann, S. / Niebauer, V. / Oberbeckmann, E. / Stoehr, G. / Schall, K. / Tosi, A. / Schwarz, M. / Buchfellner, A. / Korber, P. / Hopfner, K.P.
History
DepositionMar 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_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.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.value / _struct_conn.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin-related protein 4
B: Actin-related protein 4
C: Actin
D: Actin
E: nAct-Nanobody
F: nAct-Nanobody
G: Unknown peptide
H: Unknown peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,14112
Polymers231,0468
Non-polymers1,0954
Water2,144119
1
A: Actin-related protein 4
D: Actin
F: nAct-Nanobody
H: Unknown peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,0716
Polymers115,5234
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Actin-related protein 4
C: Actin
E: nAct-Nanobody
G: Unknown peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,0716
Polymers115,5234
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)191.224, 191.224, 221.973
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 15:229 or (resid 230 and (name...
21(chain B and (resseq 15:229 or (resid 230 and (name...
12chain E
22(chain F and resseq 3:124)
13(chain H and ((resid 3 and (name N or name...
23(chain G and ((resid 1 and (name O or name...
14(chain C and (resseq 2:40 or resseq 48:132 or (resid...
24(chain D and (resseq 2:40 or resseq 48:132 or (resid...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERLEULEU(chain A and (resseq 15:229 or (resid 230 and (name...AA15 - 22915 - 229
121TYRTYRTYRTYR(chain A and (resseq 15:229 or (resid 230 and (name...AA230230
131SERSERGLYGLY(chain A and (resseq 15:229 or (resid 230 and (name...AA15 - 47915 - 479
141SERSERGLYGLY(chain A and (resseq 15:229 or (resid 230 and (name...AA15 - 47915 - 479
151SERSERGLYGLY(chain A and (resseq 15:229 or (resid 230 and (name...AA15 - 47915 - 479
161SERSERGLYGLY(chain A and (resseq 15:229 or (resid 230 and (name...AA15 - 47915 - 479
171SERSERGLYGLY(chain A and (resseq 15:229 or (resid 230 and (name...AA15 - 47915 - 479
181SERSERGLYGLY(chain A and (resseq 15:229 or (resid 230 and (name...AA15 - 47915 - 479
191SERSERGLYGLY(chain A and (resseq 15:229 or (resid 230 and (name...AA15 - 47915 - 479
211SERSERLEULEU(chain B and (resseq 15:229 or (resid 230 and (name...BB15 - 22915 - 229
221TYRTYRTYRTYR(chain B and (resseq 15:229 or (resid 230 and (name...BB230230
231SERSERGLYGLY(chain B and (resseq 15:229 or (resid 230 and (name...BB15 - 47915 - 479
241SERSERGLYGLY(chain B and (resseq 15:229 or (resid 230 and (name...BB15 - 47915 - 479
251SERSERGLYGLY(chain B and (resseq 15:229 or (resid 230 and (name...BB15 - 47915 - 479
261SERSERGLYGLY(chain B and (resseq 15:229 or (resid 230 and (name...BB15 - 47915 - 479
271SERSERGLYGLY(chain B and (resseq 15:229 or (resid 230 and (name...BB15 - 47915 - 479
281SERSERGLYGLY(chain B and (resseq 15:229 or (resid 230 and (name...BB15 - 47915 - 479
291SERSERGLYGLY(chain B and (resseq 15:229 or (resid 230 and (name...BB15 - 47915 - 479
112GLNGLNVALVALchain EEE3 - 1243 - 124
212GLNGLNVALVAL(chain F and resseq 3:124)FF3 - 1243 - 124
113UNKUNKUNKUNK(chain H and ((resid 3 and (name N or name...HH33
123UNKUNKUNKUNK(chain H and ((resid 3 and (name N or name...HH1 - 201 - 20
133UNKUNKUNKUNK(chain H and ((resid 3 and (name N or name...HH1 - 201 - 20
213UNKUNKUNKUNK(chain G and ((resid 1 and (name O or name...GG11
223UNKUNKUNKUNK(chain G and ((resid 1 and (name O or name...GG1 - 181 - 18
233UNKUNKUNKUNK(chain G and ((resid 1 and (name O or name...GG1 - 181 - 18
114ASPASPHISHIS(chain C and (resseq 2:40 or resseq 48:132 or (resid...CC2 - 402 - 40
124GLYGLYPHEPHE(chain C and (resseq 2:40 or resseq 48:132 or (resid...CC48 - 13248 - 132
134TYRTYRTYRTYR(chain C and (resseq 2:40 or resseq 48:132 or (resid...CC133133
144ASPASPCYSCYS(chain C and (resseq 2:40 or resseq 48:132 or (resid...CC2 - 3742 - 374
154ASPASPCYSCYS(chain C and (resseq 2:40 or resseq 48:132 or (resid...CC2 - 3742 - 374
164ASPASPCYSCYS(chain C and (resseq 2:40 or resseq 48:132 or (resid...CC2 - 3742 - 374
174ASPASPCYSCYS(chain C and (resseq 2:40 or resseq 48:132 or (resid...CC2 - 3742 - 374
184ASPASPCYSCYS(chain C and (resseq 2:40 or resseq 48:132 or (resid...CC2 - 3742 - 374
194ASPASPCYSCYS(chain C and (resseq 2:40 or resseq 48:132 or (resid...CC2 - 3742 - 374
1104ASPASPCYSCYS(chain C and (resseq 2:40 or resseq 48:132 or (resid...CC2 - 3742 - 374
214ASPASPHISHIS(chain D and (resseq 2:40 or resseq 48:132 or (resid...DD2 - 402 - 40
224GLYGLYPHEPHE(chain D and (resseq 2:40 or resseq 48:132 or (resid...DD48 - 13248 - 132
234TYRTYRTYRTYR(chain D and (resseq 2:40 or resseq 48:132 or (resid...DD133133
244ASPASPCYSCYS(chain D and (resseq 2:40 or resseq 48:132 or (resid...DD2 - 3742 - 374
254ASPASPCYSCYS(chain D and (resseq 2:40 or resseq 48:132 or (resid...DD2 - 3742 - 374
264ASPASPCYSCYS(chain D and (resseq 2:40 or resseq 48:132 or (resid...DD2 - 3742 - 374
274ASPASPCYSCYS(chain D and (resseq 2:40 or resseq 48:132 or (resid...DD2 - 3742 - 374
284ASPASPCYSCYS(chain D and (resseq 2:40 or resseq 48:132 or (resid...DD2 - 3742 - 374
294ASPASPCYSCYS(chain D and (resseq 2:40 or resseq 48:132 or (resid...DD2 - 3742 - 374
2104ASPASPCYSCYS(chain D and (resseq 2:40 or resseq 48:132 or (resid...DD2 - 3742 - 374

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Actin-related protein 4 / Actin-like protein ARP4 / Actin-like protein 4


Mass: 54894.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Actin-related protein 4 ATP bound
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: ARP4, ACT3, YJL081C, J1012 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P80428
#2: Protein Actin /


Mass: 41748.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Actin is in an nucleotide free state.
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: ACT1, ABY1, END7, YFL039C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P60010

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Antibody / Protein/peptide , 2 types, 4 molecules EFGH

#3: Antibody nAct-Nanobody


Mass: 17159.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-actin and Arp4 specific nanobody with a C-terminal double Strep-Tag.
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#4: Protein/peptide Unknown peptide


Mass: 1720.111 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: We could not assign any amino acid sequence of our recombinantly expressed proteins to the electron density maps.
Source: (gene. exp.) Trichoplusia ni (cabbage looper) / Production host: Trichoplusia ni (cabbage looper)

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Non-polymers , 3 types, 123 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 5.02 Å3/Da / Density % sol: 75.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1 mM ADP, 0.2 mM CaCl2, 1.3-1.5 M sodium malonate at pH 6.0, Subtilisin (1/6000; w(subtilisin)/w(protein))

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→49.43 Å / Num. obs: 112494 / % possible obs: 99.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 57.72 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.068 / Rrim(I) all: 0.17 / Net I/σ(I): 10.4 / Num. measured all: 660887 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.8-2.8551.0921.90.5620.5311.21799.9
15.34-49.435.70.05724.60.9970.0250.06295.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.55 Å49.43 Å
Translation5.55 Å49.43 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.25data scaling
PHASER2.6.1phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YAG, 3QB0,nanobody homology model

1yag

3qb0


Resolution: 2.8→49.426 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.97
RfactorNum. reflection% reflection
Rfree0.2038 5683 5.05 %
Rwork0.1711 --
obs0.1727 112476 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 178.49 Å2 / Biso mean: 58.3069 Å2 / Biso min: 17.38 Å2
Refinement stepCycle: final / Resolution: 2.8→49.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14000 0 88 119 14207
Biso mean--40.41 48.77 -
Num. residues----1810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414370
X-RAY DIFFRACTIONf_angle_d0.70219511
X-RAY DIFFRACTIONf_chiral_restr0.0472174
X-RAY DIFFRACTIONf_plane_restr0.0042507
X-RAY DIFFRACTIONf_dihedral_angle_d10.948583
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3880X-RAY DIFFRACTION2.787TORSIONAL
12B3880X-RAY DIFFRACTION2.787TORSIONAL
21E1166X-RAY DIFFRACTION2.787TORSIONAL
22F1166X-RAY DIFFRACTION2.787TORSIONAL
31H93X-RAY DIFFRACTION2.787TORSIONAL
32G93X-RAY DIFFRACTION2.787TORSIONAL
41C3567X-RAY DIFFRACTION2.787TORSIONAL
42D3567X-RAY DIFFRACTION2.787TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.83180.3372060.290535443750100
2.8318-2.86510.30791820.279335663748100
2.8651-2.90010.30151840.2635813765100
2.9001-2.93680.31062360.255435033739100
2.9368-2.97540.26851750.252735753750100
2.9754-3.01620.30931700.239535593729100
3.0162-3.05930.32242130.243535463759100
3.0593-3.10490.29461990.23735423741100
3.1049-3.15340.27661830.235835693752100
3.1534-3.20510.29921940.214635643758100
3.2051-3.26040.25351750.204635573732100
3.2604-3.31960.25341880.197635643752100
3.3196-3.38350.22781700.193835973767100
3.3835-3.45250.25662060.193835613767100
3.4525-3.52760.22142030.180835463749100
3.5276-3.60960.19691480.172436043752100
3.6096-3.69990.16961930.154335403733100
3.6999-3.79990.1981940.153235723766100
3.7999-3.91160.18011960.157635553751100
3.9116-4.03780.18661720.14813536370899
4.0378-4.18210.17742310.140635503781100
4.1821-4.34940.16471970.13033529372699
4.3494-4.54720.14591830.12753553373699
4.5472-4.78680.16251960.129335623758100
4.7868-5.08640.14981720.142135593731100
5.0864-5.47870.19021710.151535823753100
5.4787-6.02920.18921830.17473580376399
6.0292-6.89960.19021830.17283579376299
6.8996-8.6850.1751960.1553528372498
8.685-49.43330.17641840.15883590377498

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