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- PDB-4v93: Fitted coordinates for Lumbricus terrestris hemoglobin cryo-EM co... -

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Basic information

Entry
Database: PDB / ID: 4v93
TitleFitted coordinates for Lumbricus terrestris hemoglobin cryo-EM complex (EMD-2627)
Components
  • (EXTRACELLULAR GLOBIN- ...) x 5
  • (EXTRACELLULAR HEMOGLOBIN LINKER ...) x 2
  • (HEMOGLOBIN CHAIN ...) x 2
  • HEMOGLOBIN LINKER CHAIN L1
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


hemoglobin complex / oxygen carrier activity / oxygen binding / response to hypoxia / iron ion binding / heme binding / extracellular region / metal ion binding
Similarity search - Function
Annelid erythrocruorin linker subunit, C-terminal / Erythrocruorin linker subunit, C-terminal superfamily / Extracellular hemoglobin linker subunit, heterodimerisation domain / Annelid erythrocruorin linker subunit C-terminus / Globin, extracellular / Erythrocruorin / : / Low-density lipoprotein receptor domain class A / Myoglobin-like, M family globin domain / Low-density lipoprotein (LDL) receptor class A, conserved site ...Annelid erythrocruorin linker subunit, C-terminal / Erythrocruorin linker subunit, C-terminal superfamily / Extracellular hemoglobin linker subunit, heterodimerisation domain / Annelid erythrocruorin linker subunit C-terminus / Globin, extracellular / Erythrocruorin / : / Low-density lipoprotein receptor domain class A / Myoglobin-like, M family globin domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Globin/Protoglobin / Globin domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
Extracellular globin / Extracellular globin-2 / Extracellular globin-3 / Extracellular globin-4 / Extracellular hemoglobin linker L3 subunit / Extracellular hemoglobin linker L2 subunit / Hemoglobin linker chain L1
Similarity search - Component
Biological speciesLUMBRICUS TERRESTRIS (common earthworm)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.1 Å
AuthorsChen, W.T. / Chen, Y.C. / Liou, H.H. / Chao, C.Y.
CitationJournal: Sci Rep / Year: 2015
Title: Structural basis for cooperative oxygen binding and bracelet-assisted assembly of Lumbricus terrestris hemoglobin.
Authors: Wei-Ting Chen / Yu-Chuen Chen / Horng-Huei Liou / Chih-Yu Chao /
Abstract: The iron-containing hemoglobins (Hbs) are essential proteins to serve as oxygen transporters in the blood. Among various kinds of Hbs, the earthworm Hbs are the champions in carrying oxygen due to ...The iron-containing hemoglobins (Hbs) are essential proteins to serve as oxygen transporters in the blood. Among various kinds of Hbs, the earthworm Hbs are the champions in carrying oxygen due to not only their large size but also the unusually high cooperativity of ligand binding. However, the cooperative oxygen binding mechanisms are still mostly unknown. Here we report the cryo-electron microscopy structure of Lumbricus terrestris Hb in its native, oxygenated state at 9.1 Å resolution, showing remarkable differences from the carbon monoxide-binding X-ray structure. Our structural analysis first indicates that the cooperative ligand binding of L. terrestris Hb requires tertiary and quaternary transitions in the heme pocket and a global subunit movement facilitated by intra-ring and inter-ring contacts. Moreover, the additional sinusoidal bracelet provides the confirmation for the long-standing debate about the additional electron densities absent in the X-ray crystal structure.
History
DepositionApr 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4CYX, 4D0H, 4D0I
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Other
Category: em_image_scans / pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.3Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_sheet.number_strands

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-2627
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A0: EXTRACELLULAR GLOBIN-3
A1: HEMOGLOBIN CHAIN D1
A2: EXTRACELLULAR GLOBIN-4
A3: EXTRACELLULAR GLOBIN-4
A4: EXTRACELLULAR GLOBIN-2
A5: EXTRACELLULAR GLOBIN-3
A6: HEMOGLOBIN CHAIN D1
A7: EXTRACELLULAR GLOBIN-4
AA: EXTRACELLULAR GLOBIN-4
AB: EXTRACELLULAR GLOBIN-2
AC: EXTRACELLULAR GLOBIN-3
AD: HEMOGLOBIN CHAIN D1
AE: EXTRACELLULAR GLOBIN-4
AF: EXTRACELLULAR GLOBIN-4
AG: EXTRACELLULAR GLOBIN-2
AH: EXTRACELLULAR GLOBIN-3
AI: HEMOGLOBIN CHAIN D1
AJ: EXTRACELLULAR GLOBIN-4
AK: EXTRACELLULAR GLOBIN-4
AL: EXTRACELLULAR GLOBIN-2
AM: EXTRACELLULAR GLOBIN-3
AN: HEMOGLOBIN CHAIN D1
AO: EXTRACELLULAR GLOBIN-4
AP: EXTRACELLULAR GLOBIN-4
AQ: EXTRACELLULAR GLOBIN-2
AR: EXTRACELLULAR GLOBIN-3
AS: HEMOGLOBIN CHAIN D1
AT: EXTRACELLULAR GLOBIN-4
AU: EXTRACELLULAR GLOBIN-4
AV: EXTRACELLULAR GLOBIN-2
AW: EXTRACELLULAR GLOBIN-3
AX: HEMOGLOBIN CHAIN D1
AY: EXTRACELLULAR GLOBIN-4
AZ: EXTRACELLULAR GLOBIN-4
Aa: EXTRACELLULAR GLOBIN-2
Ab: EXTRACELLULAR GLOBIN-3
Ac: HEMOGLOBIN CHAIN D1
Ad: EXTRACELLULAR GLOBIN-4
Ae: EXTRACELLULAR GLOBIN-4
Af: EXTRACELLULAR GLOBIN-2
Ag: EXTRACELLULAR GLOBIN-3
Ah: HEMOGLOBIN CHAIN D1
Ai: EXTRACELLULAR GLOBIN-4
Aj: EXTRACELLULAR GLOBIN-4
Ak: EXTRACELLULAR GLOBIN-2
Al: EXTRACELLULAR GLOBIN-3
Am: HEMOGLOBIN CHAIN D1
An: EXTRACELLULAR GLOBIN-4
Ao: EXTRACELLULAR GLOBIN-4
Ap: EXTRACELLULAR GLOBIN-2
Aq: EXTRACELLULAR GLOBIN-3
Ar: HEMOGLOBIN CHAIN D1
As: EXTRACELLULAR GLOBIN-4
At: EXTRACELLULAR GLOBIN-4
Au: EXTRACELLULAR GLOBIN-2
Av: EXTRACELLULAR GLOBIN-3
Aw: HEMOGLOBIN CHAIN D1
Ax: EXTRACELLULAR GLOBIN-4
Ay: EXTRACELLULAR GLOBIN-4
Az: EXTRACELLULAR GLOBIN-2
B0: HEMOGLOBIN CHAIN D1
B1: EXTRACELLULAR GLOBIN-4
B2: EXTRACELLULAR GLOBIN-2
B3: EXTRACELLULAR GLOBIN-2
B4: EXTRACELLULAR GLOBIN-3
B5: HEMOGLOBIN CHAIN D1
B6: EXTRACELLULAR GLOBIN-4
B7: EXTRACELLULAR GLOBIN-2
BA: EXTRACELLULAR GLOBIN-2
BB: EXTRACELLULAR GLOBIN-3
BC: HEMOGLOBIN CHAIN D1
BD: EXTRACELLULAR GLOBIN-4
BE: EXTRACELLULAR GLOBIN-2
BF: EXTRACELLULAR GLOBIN-2
BG: EXTRACELLULAR GLOBIN-3
BH: HEMOGLOBIN CHAIN D1
BI: EXTRACELLULAR GLOBIN-4
BJ: EXTRACELLULAR GLOBIN-2
BK: EXTRACELLULAR GLOBIN-2
BL: EXTRACELLULAR GLOBIN-3
BM: HEMOGLOBIN CHAIN D1
BN: EXTRACELLULAR GLOBIN-4
BO: EXTRACELLULAR GLOBIN-2
BP: EXTRACELLULAR GLOBIN-2
BQ: EXTRACELLULAR GLOBIN-3
BR: HEMOGLOBIN CHAIN D1
BS: EXTRACELLULAR GLOBIN-4
BT: EXTRACELLULAR GLOBIN-2
BU: EXTRACELLULAR GLOBIN-2
BV: EXTRACELLULAR GLOBIN-3
BW: HEMOGLOBIN CHAIN D1
BX: EXTRACELLULAR GLOBIN-4
BY: EXTRACELLULAR GLOBIN-2
BZ: EXTRACELLULAR GLOBIN-2
Ba: EXTRACELLULAR GLOBIN-3
Bb: HEMOGLOBIN CHAIN D1
Bc: EXTRACELLULAR GLOBIN-4
Bd: EXTRACELLULAR GLOBIN-2
Be: EXTRACELLULAR GLOBIN-2
Bf: EXTRACELLULAR GLOBIN-3
Bg: HEMOGLOBIN CHAIN D1
Bh: EXTRACELLULAR GLOBIN-4
Bi: EXTRACELLULAR GLOBIN-2
Bj: EXTRACELLULAR GLOBIN-2
Bk: EXTRACELLULAR GLOBIN-3
Bl: HEMOGLOBIN CHAIN D1
Bm: EXTRACELLULAR GLOBIN-4
Bn: EXTRACELLULAR GLOBIN-2
Bo: EXTRACELLULAR GLOBIN-2
Bp: EXTRACELLULAR GLOBIN-3
Bq: HEMOGLOBIN CHAIN D1
Br: EXTRACELLULAR GLOBIN-4
Bs: EXTRACELLULAR GLOBIN-2
Bt: EXTRACELLULAR GLOBIN-2
Bu: EXTRACELLULAR GLOBIN-3
Bv: HEMOGLOBIN CHAIN D1
Bw: EXTRACELLULAR GLOBIN-4
Bx: EXTRACELLULAR GLOBIN-2
By: EXTRACELLULAR GLOBIN-2
Bz: EXTRACELLULAR GLOBIN-3
C0: HEMOGLOBIN LINKER CHAIN L1
C1: EXTRACELLULAR HEMOGLOBIN LINKER L2 SUBUNIT
C2: EXTRACELLULAR HEMOGLOBIN LINKER L3 SUBUNIT
C3: EXTRACELLULAR GLOBIN-3
C4: HEMOGLOBIN CHAIN D1
C5: HEMOGLOBIN LINKER CHAIN L1
C6: EXTRACELLULAR HEMOGLOBIN LINKER L2 SUBUNIT
C7: EXTRACELLULAR HEMOGLOBIN LINKER L3 SUBUNIT
CA: EXTRACELLULAR GLOBIN-3
CB: HEMOGLOBIN CHAIN D1
CC: HEMOGLOBIN LINKER CHAIN L1
CD: EXTRACELLULAR HEMOGLOBIN LINKER L2 SUBUNIT
CE: EXTRACELLULAR HEMOGLOBIN LINKER L3 SUBUNIT
CF: EXTRACELLULAR GLOBIN-3
CG: HEMOGLOBIN CHAIN D1
CH: HEMOGLOBIN LINKER CHAIN L1
CI: EXTRACELLULAR HEMOGLOBIN LINKER L2 SUBUNIT
CJ: EXTRACELLULAR HEMOGLOBIN LINKER L3 SUBUNIT
CK: EXTRACELLULAR GLOBIN-3
CL: HEMOGLOBIN CHAIN D1
CM: HEMOGLOBIN LINKER CHAIN L1
CN: EXTRACELLULAR HEMOGLOBIN LINKER L2 SUBUNIT
CO: EXTRACELLULAR HEMOGLOBIN LINKER L3 SUBUNIT
CP: EXTRACELLULAR GLOBIN-3
CQ: HEMOGLOBIN CHAIN D1
CR: HEMOGLOBIN LINKER CHAIN L1
CS: EXTRACELLULAR HEMOGLOBIN LINKER L2 SUBUNIT
CT: EXTRACELLULAR HEMOGLOBIN LINKER L3 SUBUNIT
CU: EXTRACELLULAR GLOBIN-3
CV: HEMOGLOBIN CHAIN D1
CW: HEMOGLOBIN LINKER CHAIN L1
CX: EXTRACELLULAR HEMOGLOBIN LINKER L2 SUBUNIT
CY: EXTRACELLULAR HEMOGLOBIN LINKER L3 SUBUNIT
CZ: EXTRACELLULAR GLOBIN-3
Ca: HEMOGLOBIN CHAIN D1
Cb: HEMOGLOBIN LINKER CHAIN L1
Cc: EXTRACELLULAR HEMOGLOBIN LINKER L2 SUBUNIT
Cd: EXTRACELLULAR HEMOGLOBIN LINKER L3 SUBUNIT
Ce: EXTRACELLULAR GLOBIN-3
Cf: HEMOGLOBIN CHAIN D1
Cg: HEMOGLOBIN LINKER CHAIN L1
Ch: EXTRACELLULAR HEMOGLOBIN LINKER L2 SUBUNIT
Ci: EXTRACELLULAR HEMOGLOBIN LINKER L3 SUBUNIT
Cj: EXTRACELLULAR GLOBIN-3
Ck: HEMOGLOBIN CHAIN D1
Cl: HEMOGLOBIN LINKER CHAIN L1
Cm: EXTRACELLULAR HEMOGLOBIN LINKER L2 SUBUNIT
Cn: EXTRACELLULAR HEMOGLOBIN LINKER L3 SUBUNIT
Co: EXTRACELLULAR GLOBIN-3
Cp: HEMOGLOBIN CHAIN D1
Cq: HEMOGLOBIN LINKER CHAIN L1
Cr: EXTRACELLULAR HEMOGLOBIN LINKER L2 SUBUNIT
Cs: EXTRACELLULAR HEMOGLOBIN LINKER L3 SUBUNIT
Ct: EXTRACELLULAR GLOBIN-3
Cu: HEMOGLOBIN CHAIN D1
Cv: HEMOGLOBIN LINKER CHAIN L1
Cw: EXTRACELLULAR HEMOGLOBIN LINKER L2 SUBUNIT
Cx: EXTRACELLULAR HEMOGLOBIN LINKER L3 SUBUNIT
Cy: EXTRACELLULAR GLOBIN-3
Cz: HEMOGLOBIN CHAIN D1


Theoretical massNumber of molelcules
Total (without water)3,529,192180
Polymers3,529,192180
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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EXTRACELLULAR GLOBIN- ... , 5 types, 108 molecules A0A5ACAHAMARAWAbAgAlAqAvA2A3A7AAAEAFAJAKAOAPATAUAYAZAdAeAiAj...

#1: Protein
EXTRACELLULAR GLOBIN-3 / ERYTHROCRUORIN / EXTRACELLULAR GLOBIN III / GLOBIN C


Mass: 16902.410 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) LUMBRICUS TERRESTRIS (common earthworm) / References: UniProt: P11069
#3: Protein ...
EXTRACELLULAR GLOBIN-4 / ERYTHROCRUORIN / GLOBIN A / GLOBIN IV


Mass: 17136.619 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) LUMBRICUS TERRESTRIS (common earthworm) / References: UniProt: P13579
#4: Protein ...
EXTRACELLULAR GLOBIN-2 / ERYTHROCRUORIN / GLOBIN AIII / GLOBIN B


Mass: 16268.229 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Source: (natural) LUMBRICUS TERRESTRIS (common earthworm) / References: UniProt: P02218
#6: Protein
EXTRACELLULAR GLOBIN-4 / ERYTHROCRUORIN / GLOBIN A / GLOBIN IV


Mass: 17566.990 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) LUMBRICUS TERRESTRIS (common earthworm) / References: UniProt: P13579
#7: Protein ...
EXTRACELLULAR GLOBIN-3 / ERYTHROCRUORIN / EXTRACELLULAR GLOBIN III / GLOBIN C


Mass: 19126.137 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) LUMBRICUS TERRESTRIS (common earthworm) / References: UniProt: P11069

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HEMOGLOBIN CHAIN ... , 2 types, 36 molecules A1A6ADAIANASAXAcAhAmArAwB0B5BCBHBMBRBWBbBgBlBqBvC4CBCGCLCQCV...

#2: Protein
HEMOGLOBIN CHAIN D1


Mass: 15988.263 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) LUMBRICUS TERRESTRIS (common earthworm) / References: UniProt: O61233
#5: Protein ...
HEMOGLOBIN CHAIN D1


Mass: 17948.670 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) LUMBRICUS TERRESTRIS (common earthworm) / References: UniProt: O61233

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Protein , 1 types, 12 molecules C0C5CCCHCMCRCWCbCgClCqCv

#8: Protein
HEMOGLOBIN LINKER CHAIN L1


Mass: 27460.688 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) LUMBRICUS TERRESTRIS (common earthworm) / References: UniProt: Q9GV76

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EXTRACELLULAR HEMOGLOBIN LINKER ... , 2 types, 24 molecules C1C6CDCICNCSCXCcChCmCrCwC2C7CECJCOCTCYCdCiCnCsCx

#9: Protein
EXTRACELLULAR HEMOGLOBIN LINKER L2 SUBUNIT


Mass: 32075.490 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) LUMBRICUS TERRESTRIS (common earthworm) / References: UniProt: Q2I743
#10: Protein
EXTRACELLULAR HEMOGLOBIN LINKER L3 SUBUNIT


Mass: 26877.914 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) LUMBRICUS TERRESTRIS (common earthworm) / References: UniProt: Q2I742

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Lumbricus terrestris hemoglobin / Type: COMPLEX
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Oct 15, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 80000 X
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

SymmetryPoint symmetry: D6 (2x6 fold dihedral)
3D reconstructionResolution: 8.1 Å / Num. of particles: 4500
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD -2627. (DEPOSITION ID: 12397).
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Details: REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 2GTL

2gtl


Accession code: 2GTL / Source name: PDB / Type: experimental model
RefinementHighest resolution: 8.1 Å
Refinement stepCycle: LAST / Highest resolution: 8.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms70632 0 0 0 70632

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