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- PDB-2j59: Crystal structure of the ARF1:ARHGAP21-ArfBD complex -

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Basic information

Entry
Database: PDB / ID: 2j59
TitleCrystal structure of the ARF1:ARHGAP21-ArfBD complex
Components
  • ADP-RIBOSYLATION FACTOR 1ARF1
  • RHO-GTPASE ACTIVATING PROTEIN 10
KeywordsHYDROLASE / ARF / ARF1 / ARFBD / ARHGAP21 / MYRISTATE / TRANSPORT / NUCLEOTIDE-BINDING / RHOGAP PROTEIN / PROTEIN TRANSPORT / ACTIN ORGANIZATION / SMALL GTP-BINDING PROTEIN / GOLGI APPARATUS
Function / homology
Function and homology information


synaptic vesicle budding / lysosomal membrane organization / positive regulation of late endosome to lysosome transport / regulation of phospholipid metabolic process / maintenance of Golgi location / Golgi to transport vesicle transport / trans-Golgi Network Vesicle Budding / phospholipase D activator activity / Synthesis of PIPs at the Golgi membrane / : ...synaptic vesicle budding / lysosomal membrane organization / positive regulation of late endosome to lysosome transport / regulation of phospholipid metabolic process / maintenance of Golgi location / Golgi to transport vesicle transport / trans-Golgi Network Vesicle Budding / phospholipase D activator activity / Synthesis of PIPs at the Golgi membrane / : / Intra-Golgi traffic / Golgi localization / mitotic cleavage furrow ingression / positive regulation of ER to Golgi vesicle-mediated transport / Lysosome Vesicle Biogenesis / COPI-mediated anterograde transport / regulation of receptor internalization / very-low-density lipoprotein particle assembly / regulation of Arp2/3 complex-mediated actin nucleation / Synthesis of PIPs at the plasma membrane / COPI-dependent Golgi-to-ER retrograde traffic / positive regulation of calcium ion-dependent exocytosis / postsynaptic actin cytoskeleton organization / Golgi Associated Vesicle Biogenesis / organelle transport along microtubule / establishment of Golgi localization / MHC class II antigen presentation / RHOF GTPase cycle / dendritic spine organization / RHOD GTPase cycle / anchoring junction / regulation of small GTPase mediated signal transduction / long-term synaptic depression / RND3 GTPase cycle / positive regulation of sodium ion transmembrane transport / RHOB GTPase cycle / positive regulation of dendritic spine development / RHOJ GTPase cycle / Golgi organization / RHOC GTPase cycle / RHOQ GTPase cycle / cell leading edge / positive regulation of endocytosis / CDC42 GTPase cycle / intracellular copper ion homeostasis / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / endomembrane system / vesicle-mediated transport / RAC1 GTPase cycle / GTPase activator activity / sarcomere / small monomeric GTPase / actin filament organization / positive regulation of protein secretion / intracellular protein transport / cytoplasmic vesicle membrane / cellular response to virus / GDP binding / actin cytoskeleton / late endosome / protein transport / cell junction / postsynaptic density / neuron projection / protein domain specific binding / Golgi membrane / GTPase activity / glutamatergic synapse / GTP binding / Golgi apparatus / magnesium ion binding / signal transduction / protein-containing complex / plasma membrane / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / ADP-ribosylation factor 1-5 / PDZ domain 6 / PDZ domain / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Rho GTPase-activating protein domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / ADP-ribosylation factor 1-5 / PDZ domain 6 / PDZ domain / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Rab subfamily of small GTPases / PDZ superfamily / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / GUANOSINE-5'-TRIPHOSPHATE / ADP-ribosylation factor 1 / Rho GTPase-activating protein 21 / Rho GTPase-activating protein 21
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMenetrey, J. / Perderiset, M. / Cicolari, J. / Dubois, T. / El Khatib, N. / El Khadali, F. / Franco, M. / Chavrier, P. / Houdusse, A.
Citation
Journal: Embo J. / Year: 2007
Title: Structural Basis for Arf1-Mediated Recruitment of Arhgap21 to Golgi Membranes.
Authors: Menetrey, J. / Perderiset, M. / Cicolari, J. / Dubois, T. / El Khatib, N. / El Khadali, F. / Franco, M. / Chavrier, P. / Houdusse, A.
#1: Journal: Cryst. Growth Des. / Year: 2007
Title: Improving Diffraction from 3A to 2A for a Complex between a Small Gtpase and its Effector by Analysis of Crystal Contacts and Use of Reverse Screening.
Authors: Menetrey, J. / Perderiset, M. / Cicolari, J. / Houdusse, A. / Stura, E.A.
History
DepositionSep 13, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-RIBOSYLATION FACTOR 1
B: ADP-RIBOSYLATION FACTOR 1
C: ADP-RIBOSYLATION FACTOR 1
D: ADP-RIBOSYLATION FACTOR 1
E: ADP-RIBOSYLATION FACTOR 1
F: ADP-RIBOSYLATION FACTOR 1
M: RHO-GTPASE ACTIVATING PROTEIN 10
N: RHO-GTPASE ACTIVATING PROTEIN 10
O: RHO-GTPASE ACTIVATING PROTEIN 10
P: RHO-GTPASE ACTIVATING PROTEIN 10
Q: RHO-GTPASE ACTIVATING PROTEIN 10
R: RHO-GTPASE ACTIVATING PROTEIN 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,29536
Polymers229,98312
Non-polymers4,31224
Water29,8331656
1
A: ADP-RIBOSYLATION FACTOR 1
M: RHO-GTPASE ACTIVATING PROTEIN 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0626
Polymers38,3312
Non-polymers7324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-14.7 kcal/mol
Surface area16730 Å2
MethodPQS
2
B: ADP-RIBOSYLATION FACTOR 1
N: RHO-GTPASE ACTIVATING PROTEIN 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0626
Polymers38,3312
Non-polymers7324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-14.6 kcal/mol
Surface area16890 Å2
MethodPQS
3
D: ADP-RIBOSYLATION FACTOR 1
P: RHO-GTPASE ACTIVATING PROTEIN 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9745
Polymers38,3312
Non-polymers6443
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-14.4 kcal/mol
Surface area16820 Å2
MethodPQS
4
E: ADP-RIBOSYLATION FACTOR 1
Q: RHO-GTPASE ACTIVATING PROTEIN 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0366
Polymers38,3312
Non-polymers7064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-14.9 kcal/mol
Surface area16830 Å2
MethodPQS
5
C: ADP-RIBOSYLATION FACTOR 1
O: RHO-GTPASE ACTIVATING PROTEIN 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0987
Polymers38,3312
Non-polymers7685
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-14.7 kcal/mol
Surface area16670 Å2
MethodPQS
6
F: ADP-RIBOSYLATION FACTOR 1
R: RHO-GTPASE ACTIVATING PROTEIN 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0626
Polymers38,3312
Non-polymers7324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-13.9 kcal/mol
Surface area16890 Å2
MethodPQS
Unit cell
Length a, b, c (Å)74.636, 132.136, 146.283
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 12 molecules ABCDEFMNOPQR

#1: Protein
ADP-RIBOSYLATION FACTOR 1 / ARF1 / ARF1


Mass: 18951.615 Da / Num. of mol.: 6 / Fragment: DELTA 17-ARF1, RESIDUES 17-180 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P84078
#2: Protein
RHO-GTPASE ACTIVATING PROTEIN 10 / RHOGAP PROTEIN / ARHGAP21


Mass: 19378.922 Da / Num. of mol.: 6 / Fragment: ARF-BINDING DOMAIN, RESIDUES 929-1096
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8NI19, UniProt: Q5T5U3*PLUS

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Non-polymers , 6 types, 1680 molecules

#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H8O2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1656 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLN 70 TO LEU ENGINEERED RESIDUE IN CHAIN B, GLN 70 TO LEU ...ENGINEERED RESIDUE IN CHAIN A, GLN 70 TO LEU ENGINEERED RESIDUE IN CHAIN B, GLN 70 TO LEU ENGINEERED RESIDUE IN CHAIN C, GLN 70 TO LEU ENGINEERED RESIDUE IN CHAIN D, GLN 70 TO LEU ENGINEERED RESIDUE IN CHAIN E, GLN 70 TO LEU ENGINEERED RESIDUE IN CHAIN F, GLN 70 TO LEU

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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: 3.32 Å3/Da / Density % sol: 62.62 % / Description: NONE
Crystal growpH: 6.8
Details: 15 % PEG5000 MME, 100 MM IMIDAZOLE PH 6.8, 150 MM NH4.SO4 OR LI2SO4, 10 MM MGCL2, 0.5 % DIOXANE, 5 % ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 155860 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.6
Reflection shellResolution: 2.1→2.21 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.8 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J2I

1j2i
PDB Unreleased entry


Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.432 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS 929-930,944-955, 979-986, AND 1064-1096 FROM ARHGAP21-ARFBD WERE OMITTED FROM THE MODEL. RESIDUES FROM THE TAG IN N- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS 929-930,944-955, 979-986, AND 1064-1096 FROM ARHGAP21-ARFBD WERE OMITTED FROM THE MODEL. RESIDUES FROM THE TAG IN N-TERMINUS OF ARF1 (GS) WERE NUMBERED 16 AND 17
RfactorNum. reflection% reflectionSelection details
Rfree0.243 19925 9.9 %RANDOM
Rwork0.205 ---
obs0.209 180555 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20.06 Å2
2--0.7 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13577 0 258 1656 15491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02214085
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.96919056
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88451645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5724.085710
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.656152531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.30215120
X-RAY DIFFRACTIONr_chiral_restr0.0820.22105
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210420
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.26281
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.29448
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.21575
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.271
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.261
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6371.58597
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.073213331
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.46436463
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2444.55725
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: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.338 1368
Rwork0.277 12758

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