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- PDB-1h8e: (ADP.AlF4)2(ADP.SO4) bovine F1-ATPase (all three catalytic sites ... -

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Basic information

Entry
Database: PDB / ID: 1h8e
Title(ADP.AlF4)2(ADP.SO4) bovine F1-ATPase (all three catalytic sites occupied)
Components(BOVINE MITOCHONDRIAL F1- ...) x 5
KeywordsHYDROLASE / ATP PHOSPHORYLASE / ATP PHOSPHORYLASE (H+ TRANSPORTING) / ATP SYNTHASE / F1FO ATP SYNTHASE / F1-ATPASE
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / Mitochondrial protein degradation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex ...Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / Mitochondrial protein degradation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / aerobic respiration / ADP binding / mitochondrial inner membrane / structural molecule activity / ATP hydrolysis activity / mitochondrion / ATP binding / plasma membrane
Similarity search - Function
ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 ...ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / Pyruvate Kinase; Chain: A, domain 1 / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / Elongation Factor Tu (Ef-tu); domain 3 / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Helix Hairpins / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / ATP synthase F(1) complex catalytic subunit beta, mitochondrial / ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase F(1) complex subunit epsilon, mitochondrial / ATP synthase F(1) complex subunit alpha, mitochondrial
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMenz, R.I. / Walker, J.E. / Leslie, A.G.W.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: Structure of Bovine Mitochondrial F1-ATPase with Nucleotide Bound to All Three Catalytic Sites: Implications for the Mechanism of Rotary Catalysis
Authors: Menz, R.I. / Walker, J.E. / Leslie, A.G.W.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: The Structure of the Central Stalk in Bovine F1-ATPase at 2.4A Resolution
Authors: Gibbons, C. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
#2: Journal: Science / Year: 1999
Title: Molecular Architecture of the Rotary Motor in ATP Synthase
Authors: Stock, D. / Leslie, A.G.W. / Walker, J.E.
#3: Journal: Angew.Chem.Int.Ed.Engl. / Year: 1998
Title: ATP Synthesis by Rotary Catalysis (Nobel Lecture)
Authors: Walker, J.E.
#4: Journal: Nature / Year: 1994
Title: Structure at 2.8 A Resolution of F1-ATPase from Bovine Heart Mitochondria
Authors: Abrahams, J.P. / Leslie, A.G.W. / Lutter, R. / Walker, J.E.
#5: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization of F1-ATPase from Bovine Heart Mitochondria
Authors: Lutter, R. / Abrahams, J.P. / Van Raaij, M.J. / Todd, R.J. / Lundqvist, T. / Buchanan, S.K. / Leslie, A.G. / Walker, J.E.
History
DepositionFeb 2, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2001Provider: 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 / struct_sheet / 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 / _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 / _struct_sheet.number_strands / _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: BOVINE MITOCHONDRIAL F1-ATPASE
B: BOVINE MITOCHONDRIAL F1-ATPASE
C: BOVINE MITOCHONDRIAL F1-ATPASE
D: BOVINE MITOCHONDRIAL F1-ATPASE
E: BOVINE MITOCHONDRIAL F1-ATPASE
F: BOVINE MITOCHONDRIAL F1-ATPASE
G: BOVINE MITOCHONDRIAL F1-ATPASE
H: BOVINE MITOCHONDRIAL F1-ATPASE
I: BOVINE MITOCHONDRIAL F1-ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)375,48028
Polymers372,1009
Non-polymers3,37919
Water30,4991693
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42220 Å2
ΔGint-208.9 kcal/mol
Surface area138320 Å2
MethodPQS
Unit cell
Length a, b, c (Å)267.700, 106.200, 138.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE F1-ATPASE MOLECULE HAS THREE COPIES OF THE NON-CATALYTICALPHA SUBUNIT AND THREE COPIES OF THE CATALYTIC BETA SUBUNIT.IN THE 1994 REFERENCE, THE BETA SUBUNITS WERE LABELED ACCORDINGTO THE BOUND NUCLEOTIDE, ASBETA(DP) (BINDS ADP),BETA(E) (NO BOUND NUCLEOTIDE) ANDBETA(TP ) (AMPPNP BOUND).THE ALPHA SUBUNITS (WHICH ALL BIND AMPPNP) CONTRIBUTE TO THECATALYTIC SITES OF THE BETA SUBUNITS, AND HAVE BEEN LABELEDACCORDINGLY . THUSALPHA(DP) CONTRIBUTES TO THE CATALYTIC SITE ON BETA(DP),ALPHA(TP) TO THE SITE ON BETA ( TP) ANDALPHA(E) TO THE SITE ON BETA(E).THE CORRESPONDENCE BETWEEN THE SUBUNIT NAMES AND THE CHAINIDENTIFIERS IS GIVEN BELOW:.CHAIN A: ALPHA(E )CHAIN B: ALPHA(TP)CHAIN C: ALPHA(DP)CHAIN D : BETA(DP)CHAIN E: BETA(E)CHAIN F: BETA(TP) CHAIN G: GAMMA SUBUNITCHAIN H: DELTA SUBUNITCHAIN I: EPSILON SUBUNIT

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Components

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BOVINE MITOCHONDRIAL F1- ... , 5 types, 9 molecules ABCDEFGHI

#1: Protein BOVINE MITOCHONDRIAL F1-ATPASE / ATP SYNTHASE ALPHA CHAIN HEART ISOFORM


Mass: 55301.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P19483, EC: 3.6.1.34
#2: Protein BOVINE MITOCHONDRIAL F1-ATPASE / ATP SYNTHASE BETA CHAIN


Mass: 51757.836 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P00829, EC: 3.6.1.34
#3: Protein BOVINE MITOCHONDRIAL F1-ATPASE / ATP SYNTHASE GAMMA CHAIN


Mass: 30185.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P05631, EC: 3.6.1.34
#4: Protein BOVINE MITOCHONDRIAL F1-ATPASE / ATP SYNTHASE DELTA CHAIN


Mass: 15074.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P05630, EC: 3.6.1.34
#5: Protein/peptide BOVINE MITOCHONDRIAL F1-ATPASE / ATP SYNTHASE EPSILON CHAIN


Mass: 5662.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P05632, EC: 3.6.1.34

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Non-polymers , 6 types, 1712 molecules

#6: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#10: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1693 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsREFERENCE: 1) FOR THE ALPHA SUBUNIT: J. E. WALKER, S. J. POWELL, O. VINAS AND M. J. RUNSWICK, ...REFERENCE: 1) FOR THE ALPHA SUBUNIT: J. E. WALKER, S. J. POWELL, O. VINAS AND M. J. RUNSWICK, BIOCHEMISTRY VOL 28, PP 4702-4708, 1989. 2) FOR THE GAMMA SUBUNIT: M. R. DYER, N. J. GAY, S. J. POWELL AND J.E. WALKER, BIOCHEMISTRY VOL 28, PP 3670-3680, 1989. DIFFERENT RESIDUE: GLY A 481, GLY B 481, GLY C 481 THIS RESIDUE WAS IDENTIFIED AS A GLY FROM THE PROTEIN SEQUENCE. IN THE CDNA SEQUENCE, THE CODON FOR THIS RESIDUE WAS AGC (SER) IN THREE CLONES WHILE IN TWO OTHERS IT WAS GGC (GLY). THE DIFFERENCE WAS THOUGHT TO BE DUE TO A MUTATION OCCURRING DURING EITHER PROPAGATION OF THE CLONES IN THE LIBRARY OR SUBCLONING INTO M13 VECTORS. THE ELECTRON DENSITY SUGGESTS A GLY IN THIS POSITION. DIFFERENT RESIDUE: ASP G 273 THIS RESIDUE IS NOT PRESENT IN THE BOVINE GAMMA SUBUNIT IN THE MATERIAL USED IN THIS STRUCTURE DETERMINATION. THERE IS NO CODON FOR AN ASP IN THE CDNA SEQUENCE, NO C-TERMINAL ASP WAS FOUND IN THE PROTEIN SEQUENCE FOR THE GAMMA SUBUNIT AS ISOLATED FROM BEEF HEART MITOCHONDRIA.

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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: 2.64 Å3/Da / Density % sol: 54 %
Crystal growpH: 8
Details: CRYSTALS WERE GROWN IN THE PRESENCE OF AZIDE, A KNOWN INHIBITOR, BUT THIS HAS NOT BEEN LOCATED IN THE STRUCTURE., pH 8.00
Crystal grow
*PLUS
Temperature: 22-24 ℃ / pH: 7.2 / Method: microdialysis / Details: Lutter, R., (1993) J.Mol.Biol., 229, 787.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
199.9 %deuterium oxide11
2100 mMTris-HCl11*
314 %(w/v)PEG600011
4400 mM11*NaCl
52 mMEDTA11*
60.04 %(w/v)sodium azide11*
70.02 %(w/v)PMSF11*
810 mMdithiothreitol11*
920 mMmagnesium sulphate12
108 mM1MgCl2
110.500 mMAMP-PNP11*
120.010 mMADP11*
139 %(w/v)PEG600012
145 mM2-mercaptoethanol12
15* solutions12half of concentration * solutions

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→13.5 Å / Num. obs: 209953 / % possible obs: 79.6 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.14 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.7 / % possible all: 40.6
Reflection shell
*PLUS
% possible obs: 40.6 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE 1BMF, NATIVE BOVINE MITOCHONDRIAL F1- ATPASE

1bmf


Resolution: 2→13.5 Å / SU B: 5.8 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.21
Details: INITIAL REFINEMENT CARRIED OUT WITH TNT. ASP 270 IN CHAINS A, B, C AND THE PEPTIDE BOND BETWEEN ASP 256 AND ASN 257 IN CHAINS D, E, AND F HAVE BEEN MODELED IN A CIS CONFORMATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 9590 5 %RANDOM
Rwork0.201 ---
obs-200363 79.6 %-
Displacement parametersBiso mean: 45 Å2
Refinement stepCycle: LAST / Resolution: 2→13.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24429 0 207 1693 26329
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0250.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.0450.05
X-RAY DIFFRACTIONp_mcbond_it1.962.5
X-RAY DIFFRACTIONp_mcangle_it2.753.5
X-RAY DIFFRACTIONp_scbond_it4.715
X-RAY DIFFRACTIONp_scangle_it5.946
X-RAY DIFFRACTIONp_plane_restr0.0230.03
X-RAY DIFFRACTIONp_chiral_restr0.1240.15
X-RAY DIFFRACTIONp_singtor_nbd0.1870.3
X-RAY DIFFRACTIONp_multtor_nbd0.2090.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1920.3
X-RAY DIFFRACTIONp_planar_tor3.87
X-RAY DIFFRACTIONp_staggered_tor16.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.920
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS

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