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- PDB-6ta7: CRYSTAL STRUCTURE OF HUMAN G3BP1-NTF2 IN COMPLEX WITH HUMAN CAPRI... -

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Basic information

Entry
Database: PDB / ID: 6ta7
TitleCRYSTAL STRUCTURE OF HUMAN G3BP1-NTF2 IN COMPLEX WITH HUMAN CAPRIN1-DERIVED SOLOMON MOTIF
Components
  • Caprin-1
  • Ras GTPase-activating protein-binding protein 1
KeywordsRNA BINDING PROTEIN / Stress Granule / Complex / Regulation / Low Complexity Regions / Phase Transition
Function / homology
Function and homology information


regulation of deadenylation-dependent decapping of nuclear-transcribed mRNA / DNA/RNA helicase activity / positive regulation of stress granule assembly / intracellular mRNA localization / positive regulation of dendritic spine morphogenesis / membraneless organelle assembly / positive regulation of dendrite morphogenesis / intracellular membraneless organelle / generation of neurons / cell leading edge ...regulation of deadenylation-dependent decapping of nuclear-transcribed mRNA / DNA/RNA helicase activity / positive regulation of stress granule assembly / intracellular mRNA localization / positive regulation of dendritic spine morphogenesis / membraneless organelle assembly / positive regulation of dendrite morphogenesis / intracellular membraneless organelle / generation of neurons / cell leading edge / positive regulation of type I interferon production / ribosomal small subunit binding / signaling adaptor activity / stress granule assembly / synapse assembly / DNA helicase activity / molecular function activator activity / molecular condensate scaffold activity / P-body / negative regulation of canonical Wnt signaling pathway / cytoplasmic stress granule / lamellipodium / defense response to virus / perikaryon / endonuclease activity / DNA helicase / Ras protein signal transduction / RNA helicase activity / negative regulation of translation / RNA helicase / ribonucleoprotein complex / innate immune response / focal adhesion / mRNA binding / dendrite / synapse / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Cytoplasmic activation/proliferation-associated protein-1 C term / Cytoplasmic activation/proliferation-associated protein-1 C term / Caprin / Caprin-1 dimerization domain / Caprin-1 dimerization domain / G3BP1, RNA recognition motif / Ras GTPase-activating protein-binding protein / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 (NTF2) domain ...Cytoplasmic activation/proliferation-associated protein-1 C term / Cytoplasmic activation/proliferation-associated protein-1 C term / Caprin / Caprin-1 dimerization domain / Caprin-1 dimerization domain / G3BP1, RNA recognition motif / Ras GTPase-activating protein-binding protein / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 (NTF2) domain / Nuclear transport factor 2 domain / NTF2-like domain superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Ras GTPase-activating protein-binding protein 1 / Caprin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsSchulte, T. / Achour, A. / Panas, M.D. / McInerney, G.M.
CitationJournal: Biorxiv / Year: 2021
Title: Caprin-1 binding to the critical stress granule protein G3BP1 is regulated by pH
Authors: Schulte, T. / Panas, M.D. / Williams, L. / Kedersha, N. / Fleck, J.S. / Tan, T.J. / Olsson, A. / Morro, A.M. / Hanke, L. / Nilvebrant, J. / Giang, K.A. / Nygren, P.A. / Anderson, P. / ...Authors: Schulte, T. / Panas, M.D. / Williams, L. / Kedersha, N. / Fleck, J.S. / Tan, T.J. / Olsson, A. / Morro, A.M. / Hanke, L. / Nilvebrant, J. / Giang, K.A. / Nygren, P.A. / Anderson, P. / Achour, A. / McInerney, G.M.
History
DepositionOct 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Ras GTPase-activating protein-binding protein 1
B: Ras GTPase-activating protein-binding protein 1
D: Ras GTPase-activating protein-binding protein 1
F: Ras GTPase-activating protein-binding protein 1
G: Caprin-1
H: Caprin-1
C: Ras GTPase-activating protein-binding protein 1
E: Ras GTPase-activating protein-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,46911
Polymers103,3878
Non-polymers813
Water4,954275
1
A: Ras GTPase-activating protein-binding protein 1
hetero molecules

E: Ras GTPase-activating protein-binding protein 1


  • defined by author
  • Evidence: isothermal titration calorimetry, Caprin-derived Solomon motif fused to GFP bound to NTF2 with affinity of about 1 uM. Single-residue mutations of Caprin and NTF2-like domain confirmed ...Evidence: isothermal titration calorimetry, Caprin-derived Solomon motif fused to GFP bound to NTF2 with affinity of about 1 uM. Single-residue mutations of Caprin and NTF2-like domain confirmed observed binding interface. Described in detail in associated manuscript.
  • 32 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)31,9953
Polymers31,9722
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_444x-1/2,-y-1/2,-z-11
2
B: Ras GTPase-activating protein-binding protein 1
F: Ras GTPase-activating protein-binding protein 1
H: Caprin-1


  • defined by author
  • Evidence: isothermal titration calorimetry, Caprin-derived Solomon motif fused to GFP bound to NTF2 with affinity of about 1 uM. Single-residue mutations of Caprin and NTF2-like domain confirmed ...Evidence: isothermal titration calorimetry, Caprin-derived Solomon motif fused to GFP bound to NTF2 with affinity of about 1 uM. Single-residue mutations of Caprin and NTF2-like domain confirmed observed binding interface. Described in detail in associated manuscript.
  • 35.7 kDa, 3 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)35,7073
Polymers35,7073
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Ras GTPase-activating protein-binding protein 1
G: Caprin-1
C: Ras GTPase-activating protein-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7665
Polymers35,7073
Non-polymers582
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.558, 100.038, 113.345
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32

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
111LYSLYSVALVAL(chain 'A' and ((resid 5 and (name N or name...AA5 - 166 - 17
121GLNGLNHISHIS(chain 'A' and ((resid 5 and (name N or name...AA18 - 3119 - 32
131PHEPHELEULEU(chain 'A' and ((resid 5 and (name N or name...AA33 - 4534 - 46
141LYSLYSGLNGLN(chain 'A' and ((resid 5 and (name N or name...AA50 - 5851 - 59
151GLUGLUHISHIS(chain 'A' and ((resid 5 and (name N or name...AA60 - 6261 - 63
161LYSLYSCYSCYS(chain 'A' and ((resid 5 and (name N or name...AA64 - 7365 - 74
171THRTHRTHRTHR(chain 'A' and ((resid 5 and (name N or name...AA7576
181ILEILEVALVAL(chain 'A' and ((resid 5 and (name N or name...AA77 - 8078 - 81
191ALAALAPROPRO(chain 'A' and ((resid 5 and (name N or name...AA82 - 11683 - 117
1101TYRTYRPHEPHE(chain 'A' and ((resid 5 and (name N or name...AA125 - 138126 - 139
2111LYSLYSVALVAL(chain 'B' and (resid 5 through 16 or resid 18...BB5 - 166 - 17
2121GLNGLNHISHIS(chain 'B' and (resid 5 through 16 or resid 18...BB18 - 3119 - 32
2131PHEPHELEULEU(chain 'B' and (resid 5 through 16 or resid 18...BB33 - 4534 - 46
2141LYSLYSGLNGLN(chain 'B' and (resid 5 through 16 or resid 18...BB50 - 5851 - 59
2151GLUGLUHISHIS(chain 'B' and (resid 5 through 16 or resid 18...BB60 - 6261 - 63
2161LYSLYSCYSCYS(chain 'B' and (resid 5 through 16 or resid 18...BB64 - 7365 - 74
2171THRTHRTHRTHR(chain 'B' and (resid 5 through 16 or resid 18...BB7576
2181ILEILEVALVAL(chain 'B' and (resid 5 through 16 or resid 18...BB77 - 8078 - 81
2191ALAALAPROPRO(chain 'B' and (resid 5 through 16 or resid 18...BB82 - 11683 - 117
2201TYRTYRPHEPHE(chain 'B' and (resid 5 through 16 or resid 18...BB125 - 138126 - 139
3211LYSLYSVALVAL(chain 'C' and (resid 5 through 16 or resid 18...CG5 - 166 - 17
3221GLNGLNHISHIS(chain 'C' and (resid 5 through 16 or resid 18...CG18 - 3119 - 32
3231PHEPHELEULEU(chain 'C' and (resid 5 through 16 or resid 18...CG33 - 4534 - 46
3241LYSLYSGLNGLN(chain 'C' and (resid 5 through 16 or resid 18...CG50 - 5851 - 59
3251GLUGLUHISHIS(chain 'C' and (resid 5 through 16 or resid 18...CG60 - 6261 - 63
3261LYSLYSCYSCYS(chain 'C' and (resid 5 through 16 or resid 18...CG64 - 7365 - 74
3271THRTHRTHRTHR(chain 'C' and (resid 5 through 16 or resid 18...CG7576
3281ILEILEVALVAL(chain 'C' and (resid 5 through 16 or resid 18...CG77 - 8078 - 81
3291ALAALAPROPRO(chain 'C' and (resid 5 through 16 or resid 18...CG82 - 11683 - 117
3301TYRTYRPHEPHE(chain 'C' and (resid 5 through 16 or resid 18...CG125 - 138126 - 139
1312GLUGLUARGARG(chain 'D' and (resid 4 through 13 or resid 15...DC4 - 135 - 14
1322PHEPHEARGARG(chain 'D' and (resid 4 through 13 or resid 15...DC15 - 1716 - 18
1332TYRTYRHISHIS(chain 'D' and (resid 4 through 13 or resid 15...DC19 - 3120 - 32
1342PHEPHEHISHIS(chain 'D' and (resid 4 through 13 or resid 15...DC33 - 4234 - 43
1352ALAALAGLNGLN(chain 'D' and (resid 4 through 13 or resid 15...DC52 - 5853 - 59
1362ILEILEHISHIS(chain 'D' and (resid 4 through 13 or resid 15...DC61 - 6262 - 63
1372LYSLYSCYSCYS(chain 'D' and (resid 4 through 13 or resid 15...DC64 - 7365 - 74
1382THRTHRGLNGLN(chain 'D' and (resid 4 through 13 or resid 15...DC75 - 10376 - 104
1392ARGARGPHEPHE(chain 'D' and (resid 4 through 13 or resid 15...DC106 - 108107 - 109
1402GLNGLNPROPRO(chain 'D' and (resid 4 through 13 or resid 15...DC110 - 116111 - 117
1412ALAALATYRTYR(chain 'D' and (resid 4 through 13 or resid 15...DC121 - 133122 - 134
2422GLUGLUARGARG(chain 'E' and (resid 4 or (resid 5 and (name...EH4 - 135 - 14
2432PHEPHEARGARG(chain 'E' and (resid 4 or (resid 5 and (name...EH15 - 1716 - 18
2442TYRTYRHISHIS(chain 'E' and (resid 4 or (resid 5 and (name...EH19 - 3120 - 32
2452PHEPHEHISHIS(chain 'E' and (resid 4 or (resid 5 and (name...EH33 - 4234 - 43
2462ALAALAGLNGLN(chain 'E' and (resid 4 or (resid 5 and (name...EH52 - 5853 - 59
2472ILEILEHISHIS(chain 'E' and (resid 4 or (resid 5 and (name...EH61 - 6262 - 63
2482LYSLYSCYSCYS(chain 'E' and (resid 4 or (resid 5 and (name...EH64 - 7365 - 74
2492THRTHRGLNGLN(chain 'E' and (resid 4 or (resid 5 and (name...EH75 - 10376 - 104
2502ARGARGPHEPHE(chain 'E' and (resid 4 or (resid 5 and (name...EH106 - 108107 - 109
2512GLNGLNPROPRO(chain 'E' and (resid 4 or (resid 5 and (name...EH110 - 116111 - 117
2522ALAALATYRTYR(chain 'E' and (resid 4 or (resid 5 and (name...EH121 - 133122 - 134
3532GLUGLUARGARG(chain 'F' and ((resid 4 and (name N or name...FD4 - 135 - 14
3542PHEPHEARGARG(chain 'F' and ((resid 4 and (name N or name...FD15 - 1716 - 18
3552TYRTYRHISHIS(chain 'F' and ((resid 4 and (name N or name...FD19 - 3120 - 32
3562PHEPHEHISHIS(chain 'F' and ((resid 4 and (name N or name...FD33 - 4234 - 43
3572ALAALAGLNGLN(chain 'F' and ((resid 4 and (name N or name...FD52 - 5853 - 59
3582ILEILEHISHIS(chain 'F' and ((resid 4 and (name N or name...FD61 - 6262 - 63
3592LYSLYSCYSCYS(chain 'F' and ((resid 4 and (name N or name...FD64 - 7365 - 74
3602THRTHRGLNGLN(chain 'F' and ((resid 4 and (name N or name...FD75 - 10376 - 104
3612ARGARGPHEPHE(chain 'F' and ((resid 4 and (name N or name...FD106 - 108107 - 109
3622GLNGLNPROPRO(chain 'F' and ((resid 4 and (name N or name...FD110 - 116111 - 117
3632ALAALATYRTYR(chain 'F' and ((resid 4 and (name N or name...FD121 - 133122 - 134

NCS ensembles :
ID
1
2

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Components

#1: Protein
Ras GTPase-activating protein-binding protein 1 / G3BP-1 / ATP-dependent DNA helicase VIII / hDH VIII / GAP SH3 domain-binding protein 1


Mass: 15986.153 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G3BP1, G3BP / Production host: Escherichia coli (E. coli) / References: UniProt: Q13283, DNA helicase, RNA helicase
#2: Protein/peptide Caprin-1 / Cell cycle-associated protein 1 / Cytoplasmic activation- and proliferation-associated protein 1 / ...Cell cycle-associated protein 1 / Cytoplasmic activation- and proliferation-associated protein 1 / GPI-anchored membrane protein 1 / GPI-anchored protein p137 / p137GPI / Membrane component chromosome 11 surface marker 1 / RNA granule protein 105


Mass: 3735.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14444
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium chloride, 0.1M Tris 8.0, 20% w/v PEG 4000 of the Proplex crystallization screen (Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.928→46.54 Å / Num. obs: 66520 / % possible obs: 94.26 % / Redundancy: 13.5 % / Biso Wilson estimate: 40.02 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.62
Reflection shellResolution: 1.928→1.997 Å / Mean I/σ(I) obs: 0.68 / Num. unique obs: 4630 / CC1/2: 0.32 / % possible all: 66.43

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.14_3260refinement
Cootmodel building
MxCuBEdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FW5

5fw5


Resolution: 1.93→46.54 Å / SU ML: 0.262 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0378
RfactorNum. reflection% reflection
Rfree0.2518 2098 3.15 %
Rwork0.2067 --
obs0.2081 66504 94.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 60.84 Å2
Refinement stepCycle: LAST / Resolution: 1.93→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6230 0 3 275 6508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00676392
X-RAY DIFFRACTIONf_angle_d0.77738627
X-RAY DIFFRACTIONf_chiral_restr0.051905
X-RAY DIFFRACTIONf_plane_restr0.00521141
X-RAY DIFFRACTIONf_dihedral_angle_d16.75032279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.970.441920.3872829X-RAY DIFFRACTION63.01
1.97-2.020.3811120.3373457X-RAY DIFFRACTION76.46
2.02-2.080.35831380.30444212X-RAY DIFFRACTION93.83
2.08-2.140.29311440.27184422X-RAY DIFFRACTION98.02
2.14-2.210.29641440.25374414X-RAY DIFFRACTION98.23
2.21-2.290.31351440.24084445X-RAY DIFFRACTION98.35
2.29-2.380.24581420.23614377X-RAY DIFFRACTION97.06
2.38-2.490.2751460.22554464X-RAY DIFFRACTION98.06
2.49-2.620.25071450.22494464X-RAY DIFFRACTION98.63
2.62-2.780.31451460.22264474X-RAY DIFFRACTION98.76
2.78-30.25251450.2184431X-RAY DIFFRACTION97.24
3-3.30.23571480.20844541X-RAY DIFFRACTION99.26
3.3-3.770.25081490.18944565X-RAY DIFFRACTION99.18
3.77-4.750.22931480.15714564X-RAY DIFFRACTION98.39
4.75-46.540.21471550.20254747X-RAY DIFFRACTION98.26

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