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- PDB-4bsr: Structure of the ectodomain of LGR5 in complex with R-spondin-1 (... -

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Basic information

Entry
Database: PDB / ID: 4bsr
TitleStructure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P22121 crystal form
Components
  • LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
  • R-SPONDIN-1
KeywordsSIGNALING PROTEIN / ADULT STEM CELL / LEUCINE-RICH REPEAT G-PROTEIN COUPLED RECEPTOR / LEUCINE-RICH REPEAT / FURIN DOMAIN / WNT SIGNALING / CONGENITAL ANONYCHIA
Function / homology
Function and homology information


epithelial cell proliferation involved in renal tubule morphogenesis / oocyte differentiation / protein-hormone receptor activity / regulation of receptor internalization / G protein-coupled peptide receptor activity / inner ear development / positive regulation of Wnt signaling pathway / hair follicle development / Regulation of FZD by ubiquitination / trans-Golgi network membrane ...epithelial cell proliferation involved in renal tubule morphogenesis / oocyte differentiation / protein-hormone receptor activity / regulation of receptor internalization / G protein-coupled peptide receptor activity / inner ear development / positive regulation of Wnt signaling pathway / hair follicle development / Regulation of FZD by ubiquitination / trans-Golgi network membrane / G protein-coupled receptor activity / G protein-coupled receptor binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Wnt signaling pathway / positive regulation of canonical Wnt signaling pathway / transmembrane signaling receptor activity / heparin binding / regulation of cell population proliferation / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / signaling receptor binding / Golgi apparatus / extracellular region / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
R-spondin, Fu-CRD domain / Furin-like repeat, cysteine-rich / Glycoprotein hormone receptor family / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. ...R-spondin, Fu-CRD domain / Furin-like repeat, cysteine-rich / Glycoprotein hormone receptor family / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / Alpha-Beta Horseshoe / Furin-like repeat / Furin-like repeats / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Growth factor receptor cysteine-rich domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Ribbon / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Leucine-rich repeat-containing G-protein coupled receptor 5 / R-spondin-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.2 Å
AuthorsPeng, W.C. / de Lau, W. / Forneris, F. / Granneman, J.C.M. / Huch, M. / Clevers, H. / Gros, P.
CitationJournal: Cell Rep. / Year: 2013
Title: Structure of Stem Cell Growth Factor R-Spondin 1 in Complex with the Ectodomain of its Receptor Lgr5.
Authors: Peng, W.C. / De Lau, W. / Forneris, F. / Granneman, J.C.M. / Huch, M. / Clevers, H. / Gros, P.
History
DepositionJun 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
B: LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
C: R-SPONDIN-1
D: R-SPONDIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,2279
Polymers148,1464
Non-polymers2,0815
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9990 Å2
ΔGint-18.9 kcal/mol
Surface area54630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.175, 143.779, 167.338
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5 / G-PROTEIN COUPLED RECEPTOR 49 / G-PROTEIN COUPLED RECEPTOR 67 / G-PROTEIN COUPLED RECEPTOR HG38


Mass: 60366.457 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR LRR DOMAIN, RESIDUES 22-543
Source method: isolated from a genetically manipulated source
Details: N-LINKED GLYCOSYLATIONS AT ASN 63,77,208,500 / Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: O75473
#2: Protein R-SPONDIN-1 / ROOF PLATE-SPECIFIC SPONDIN-1 / HRSPO1


Mass: 13706.780 Da / Num. of mol.: 2 / Fragment: FU1FU2, RESIDUES 31-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q2MKA7
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Sequence detailsN-TERMINAL 6XHISTAG, PLUS ENLYFQGS AND C-TERMINAL AAA INTRODUCED BY CLONING N-TERMINAL GS AND C- ...N-TERMINAL 6XHISTAG, PLUS ENLYFQGS AND C-TERMINAL AAA INTRODUCED BY CLONING N-TERMINAL GS AND C-TERMINAL AAA ADDED BY CLONING PLASMID, PLUS C-TERMINAL 6XHIS TAG

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.52 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→47.9 Å / Num. obs: 34548 / % possible obs: 99.7 % / Observed criterion σ(I): 1.4 / Redundancy: 3.7 % / Biso Wilson estimate: 69.78 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.2

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.2→46.074 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 27.64 / Stereochemistry target values: ML
Details: EXTENDED C-TERMINAL REGION MODELLED WITH ZERO OCCUPANCY
RfactorNum. reflection% reflection
Rfree0.2576 1735 5 %
Rwork0.2309 --
obs0.2322 34464 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.9 Å2
Refinement stepCycle: LAST / Resolution: 3.2→46.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9137 0 137 0 9274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039552
X-RAY DIFFRACTIONf_angle_d0.91212950
X-RAY DIFFRACTIONf_dihedral_angle_d17.5893524
X-RAY DIFFRACTIONf_chiral_restr0.0341516
X-RAY DIFFRACTIONf_plane_restr0.0041660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.29420.36181630.35482669X-RAY DIFFRACTION100
3.2942-3.40050.3421260.32422722X-RAY DIFFRACTION100
3.4005-3.5220.3381340.322672X-RAY DIFFRACTION99
3.522-3.66290.29431470.27792677X-RAY DIFFRACTION99
3.6629-3.82950.29661400.24052712X-RAY DIFFRACTION100
3.8295-4.03130.29491340.22022699X-RAY DIFFRACTION100
4.0313-4.28370.22951420.21682747X-RAY DIFFRACTION100
4.2837-4.61420.22491670.19312684X-RAY DIFFRACTION100
4.6142-5.0780.19981370.18932738X-RAY DIFFRACTION99
5.078-5.81160.23861360.2092759X-RAY DIFFRACTION100
5.8116-7.31730.26761420.22472780X-RAY DIFFRACTION99
7.3173-46.07870.22541670.2082870X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6745-0.02670.19890.0072-0.02440.2104-0.54370.2758-0.0989-0.4519-0.01060.37-0.15590.0281-0.26250.58510.23350.02360.5262-0.27450.5556-33.8519-98.59399.0883
20.10160.0436-0.00480.01530.04760.0922-0.27230.3837-0.6669-0.2054-0.24520.41340.05190.071-0.02030.28280.06740.02140.526-0.1220.4047-35.7228-99.485418.2259
30.2864-0.0552-0.05561.25340.33630.03330.01450.005-0.07650.1618-0.1408-0.00190.12090.0087-0.00490.33060.01770.02810.30.0280.334-19.0827-70.490537.1616
40.19050.08170.09410.44370.02790.6627-0.1559-0.050.0819-0.5672-0.1029-0.04050.146-0.1897-1.34880.53360.0323-0.02670.20550.160.1193-10.1604-30.959214.9215
50.7505-0.43720.31930.9615-0.20240.57560.13950.6004-0.3932-1.0964-0.4320.3959-0.18760.4395-0.9280.3997-0.17380.27390.23020.0836-0.0262-5.749613.750712.424
60.0924-0.0547-0.31871.7354-0.33080.33760.18130.01490.0807-0.0277-0.19290.22-0.19850.08090.05960.26060.07290.0210.30150.05630.2841-26.5678-22.246932.7525
7-0.03410.02060.0971-0.012-0.0307-0.0201-0.7238-0.66440.01810.0477-0.24150.1262-0.0380.5858-0.00331.7956-0.08020.28221.02850.07981.1144-24.8222-39.72282.9552
80.01-0.0199-0.0119-0.0011-0.0070.0052-0.30730.34410.0546-0.3018-0.01020.286-0.16990.0649-0.00030.8713-0.0504-0.20171.00580.24930.8012-40.4906-70.451412.6579
90.0087-0.00420.00630.005-0.00140.00910.0646-0.11880.0164-0.11050.08730.0577-0.0297-0.1539-01.1710.06980.01941.00450.15880.7018-31.6966-73.820614.9375
100.0296-0.01830.00380.0062-0.00090.0045-0.0844-0.1470.0675-0.0358-0.0568-0.02450.02540.09930.00011.75120.01560.46911.1369-0.05981.0992-25.684-66.74735.3166
110.0445-0.00430.0320.0107-0.01870.0464-0.19250.15460.0041-0.2207-0.183-0.03380.03540.0094-0.00610.76470.12340.44170.7891-0.48720.8927-30.8174-78.096413.8081
120.05550.01330.14860.090.10670.1683-0.13360.13360.238-0.13680.0983-0.3217-0.06720.1568-0.00020.47490.08480.15720.3889-0.02650.5213-18.0086-80.03722.2453
13-0.0052-0.0033-0.00160.0015-00.0060.1616-0.1481-0.07870.02050.1093-0.14230.104-0.01010.00060.77340.3416-0.23711.26490.15321.3861-1.8624-89.55929.3614
140.00090.0007-0.00230.0007-0.0021-00.11960.08970.03190.09070.00420.0407-0.1002-0.0030.00021.12310.00160.04451.0955-0.00171.1431-8.4843-95.202725.5011
150.01490.0029-0.0013-0.0005-0.0004-0.00140.1081-0.0485-0.0880.01180.0688-0.1499-0.0814-0.02640.00020.60670.15890.19030.5802-0.12431.03010.8173-13.93039.2932
160.0125-0.00160.00340.01880.01640.0118-0.02690.02440.03340.2509-0.1499-0.1967-0.34230.0147-00.30530.0628-0.05120.3231-0.04960.3144-3.0205-13.493114.2953
170.0492-0.03390.08910.0213-0.06640.3968-0.0266-0.0531-0.2079-0.20910.01040.38710.2998-0.2209-0.15320.4121-0.1682-0.18980.47260.06780.2504-12.2702-12.99739.7438
180.11480.04830.07570.04620.09860.2956-0.19990.23930.1056-0.0761-0.00760.09460.0095-0.0493-0.1070.6044-0.0559-0.20060.3090.16260.3329-11.3114-11.13158.9278
190.03320.0558-0.00360.067-0.01070.0089-0.1447-0.3581-0.06660.2288-0.15580.06610.2370.031-0.10320.7262-0.05130.07250.4202-0.0050.061-11.3919-10.144221.64
200.0750.01770.0589-0.01070.02120.0581-0.10870.0849-0.0234-0.16670.02560.1866-0.0062-0.3687-0.0562-0.0033-0.4144-0.08820.1939-0.25250.6859-23.8544-8.79216.2189
210.0081-0.0124-0.00880.01830.01770.002-0.21650.1867-0.0589-0.0112-0.0112-0.10570.0995-0.02270.00040.6461-0.00380.05320.46630.06620.4042-24.106-3.670120.9797
220.0458-0.0203-0.03670.01680.01050.0960.13750.12030.24940.05670.35520.3819-0.1455-0.2260.04140.90280.3346-0.34430.55090.19310.4344-31.63271.923519.2504
230.0002-0.0038-0.00860.04270.10220.3537-0.0458-0.15170.05580.09310.04820.0131-0.029-0.03090.00510.79890.7539-0.64041.43150.18691.1517-40.49984.149624.1557
240.01010.0184-0.03950.0317-0.06220.24720.01660.0322-0.05390.02340.01360.00080.016-0.0037-0.00052.0852-0.34980.11981.94340.36522.2577-37.925311.232126.0692
250.0009-0.00210.00360.0019-0.00460.0065-0.0134-0.03410.1042-0.0554-0.02290.07920.0154-0.047700.8570.1993-0.01140.7501-0.19951.1005-32.809810.935819.8637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN B AND (RESID 31 THROUGH 66 )
2X-RAY DIFFRACTION2CHAIN B AND (RESID 67 THROUGH 92 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 93 THROUGH 401 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 402 THROUGH 543 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 28 THROUGH 111 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 112 THROUGH 482 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 483 THROUGH 543 )
8X-RAY DIFFRACTION8CHAIN D AND (RESID 40 THROUGH 59 )
9X-RAY DIFFRACTION9CHAIN D AND (RESID 60 THROUGH 65 )
10X-RAY DIFFRACTION10CHAIN D AND (RESID 66 THROUGH 71 )
11X-RAY DIFFRACTION11CHAIN D AND (RESID 72 THROUGH 82 )
12X-RAY DIFFRACTION12CHAIN D AND (RESID 83 THROUGH 126 )
13X-RAY DIFFRACTION13CHAIN D AND (RESID 127 THROUGH 136 )
14X-RAY DIFFRACTION14CHAIN D AND (RESID 137 THROUGH 143 )
15X-RAY DIFFRACTION15CHAIN C AND (RESID 40 THROUGH 49 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 50 THROUGH 60 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 61 THROUGH 67 )
18X-RAY DIFFRACTION18CHAIN C AND (RESID 68 THROUGH 82 )
19X-RAY DIFFRACTION19CHAIN C AND (RESID 83 THROUGH 92 )
20X-RAY DIFFRACTION20CHAIN C AND (RESID 93 THROUGH 101 )
21X-RAY DIFFRACTION21CHAIN C AND (RESID 102 THROUGH 111 )
22X-RAY DIFFRACTION22CHAIN C AND (RESID 112 THROUGH 126 )
23X-RAY DIFFRACTION23CHAIN C AND (RESID 127 THROUGH 131 )
24X-RAY DIFFRACTION24CHAIN C AND (RESID 132 THROUGH 136 )
25X-RAY DIFFRACTION25CHAIN C AND (RESID 137 THROUGH 142 )

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  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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