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- PDB-4jqi: Structure of active beta-arrestin1 bound to a G protein-coupled r... -

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Basic information

Entry
Database: PDB / ID: 4jqi
TitleStructure of active beta-arrestin1 bound to a G protein-coupled receptor phosphopeptide
Components
  • Beta-arrestin-1Arrestin
  • Fab30 heavy chain
  • Fab30 light chain
  • Vasopressin V2 receptor phosphopeptide
KeywordsSIGNALING PROTEIN / Arrestin / GPCR / G-protein coupled receptor / signaling
Function / homology
Function and homology information


V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / Activation of SMO / sensory perception of touch / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / G alpha (s) signalling events / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin ...V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / Activation of SMO / sensory perception of touch / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / G alpha (s) signalling events / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / alpha-1B adrenergic receptor binding / follicle-stimulating hormone signaling pathway / protein phosphorylated amino acid binding / angiotensin receptor binding / AP-2 adaptor complex binding / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / MAP2K and MAPK activation / Ub-specific processing proteases / positive regulation of systemic arterial blood pressure / hemostasis / telencephalon development / positive regulation of smooth muscle cell apoptotic process / negative regulation of interleukin-8 production / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / regulation of G protein-coupled receptor signaling pathway / arrestin family protein binding / G protein-coupled receptor internalization / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of intracellular signal transduction / mitogen-activated protein kinase kinase binding / positive regulation of Rho protein signal transduction / clathrin binding / stress fiber assembly / negative regulation of Notch signaling pathway / pseudopodium / positive regulation of insulin secretion involved in cellular response to glucose stimulus / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / negative regulation of interleukin-6 production / positive regulation of receptor internalization / phototransduction / endocytic vesicle / clathrin-coated pit / positive regulation of vasoconstriction / negative regulation of protein ubiquitination / cellular response to hormone stimulus / insulin-like growth factor receptor binding / activation of adenylate cyclase activity / visual perception / GTPase activator activity / negative regulation of protein phosphorylation / positive regulation of protein ubiquitination / G protein-coupled receptor binding / response to cytokine / nuclear estrogen receptor binding / phosphoprotein binding / peptide binding / clathrin-coated endocytic vesicle membrane / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / Vasopressin regulates renal water homeostasis via Aquaporins / endocytosis / protein transport / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of peptidyl-serine phosphorylation / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / G alpha (s) signalling events / postsynaptic membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / basolateral plasma membrane / regulation of apoptotic process / negative regulation of neuron apoptotic process / transmembrane transporter binding / dendritic spine / positive regulation of MAPK cascade / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / protein ubiquitination / endosome / response to xenobiotic stimulus / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / signaling receptor binding / ubiquitin protein ligase binding / positive regulation of cell population proliferation / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / endoplasmic reticulum
Similarity search - Function
Immunoglobulin-like - #840 / Vasopressin V2 receptor / Immunoglobulin-like - #640 / Vasopressin receptor / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain ...Immunoglobulin-like - #840 / Vasopressin V2 receptor / Immunoglobulin-like - #640 / Vasopressin receptor / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PROLINE / Beta-arrestin-1 / Vasopressin V2 receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsShukla, A.K. / Manglik, A. / Kruse, A.C. / Xiao, K. / Reis, R.I. / Tseng, W.C. / Staus, D.P. / Hilger, D. / Uysal, S. / Huang, L.H. ...Shukla, A.K. / Manglik, A. / Kruse, A.C. / Xiao, K. / Reis, R.I. / Tseng, W.C. / Staus, D.P. / Hilger, D. / Uysal, S. / Huang, L.H. / Paduch, M. / Shukla, P.T. / Koide, A. / Koide, S. / Weis, W.I. / Kossiakoff, A.A. / Kobilka, B.K. / Lefkowitz, R.J.
CitationJournal: Nature / Year: 2013
Title: Structure of active beta-arrestin-1 bound to a G-protein-coupled receptor phosphopeptide.
Authors: Shukla, A.K. / Manglik, A. / Kruse, A.C. / Xiao, K. / Reis, R.I. / Tseng, W.C. / Staus, D.P. / Hilger, D. / Uysal, S. / Huang, L.Y. / Paduch, M. / Tripathi-Shukla, P. / Koide, A. / Koide, S. ...Authors: Shukla, A.K. / Manglik, A. / Kruse, A.C. / Xiao, K. / Reis, R.I. / Tseng, W.C. / Staus, D.P. / Hilger, D. / Uysal, S. / Huang, L.Y. / Paduch, M. / Tripathi-Shukla, P. / Koide, A. / Koide, S. / Weis, W.I. / Kossiakoff, A.A. / Kobilka, B.K. / Lefkowitz, R.J.
History
DepositionMar 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Beta-arrestin-1
H: Fab30 heavy chain
L: Fab30 light chain
V: Vasopressin V2 receptor phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,11213
Polymers97,5544
Non-polymers5589
Water1,946108
1
A: Beta-arrestin-1
V: Vasopressin V2 receptor phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7044
Polymers48,6062
Non-polymers982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: Fab30 heavy chain
L: Fab30 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4089
Polymers48,9472
Non-polymers4617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8820 Å2
ΔGint-57 kcal/mol
Surface area35520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.840, 125.128, 144.203
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody Fab30 heavy chain


Mass: 25512.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): 55244
#3: Antibody Fab30 light chain


Mass: 23435.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): 55244

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Protein / Protein/peptide , 2 types, 2 molecules AV

#1: Protein Beta-arrestin-1 / Arrestin / Arrestin beta-1


Mass: 45055.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arrb1 / Plasmid: pGEX4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29066
#4: Protein/peptide Vasopressin V2 receptor phosphopeptide


Mass: 3550.936 Da / Num. of mol.: 1 / Fragment: unp residues 343-371 / Source method: obtained synthetically / References: UniProt: P30518

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Non-polymers , 4 types, 117 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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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: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17% PEG 3350, 0.1 M HEPES, 0.2 M L-proline , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 28, 2012 / Details: Mirrors
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.6→39.3 Å / Num. obs: 32184 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rsym value: 0.087
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 3517 / Rsym value: 0.72 / % possible all: 97.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JSY, 3EFF

1jsy

3eff


Resolution: 2.6→39.281 Å / SU ML: 0.35 / σ(F): 1.33 / Phase error: 26.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 1628 5.06 %RANDOM
Rwork0.2006 ---
obs0.2029 32184 98.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→39.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5716 0 34 108 5858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045884
X-RAY DIFFRACTIONf_angle_d0.7858031
X-RAY DIFFRACTIONf_dihedral_angle_d11.3082077
X-RAY DIFFRACTIONf_chiral_restr0.05924
X-RAY DIFFRACTIONf_plane_restr0.0031020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.67650.34911380.29032465X-RAY DIFFRACTION97
2.6765-2.76290.29341280.26542543X-RAY DIFFRACTION99
2.7629-2.86160.29781290.23472550X-RAY DIFFRACTION99
2.8616-2.97610.3061410.23132517X-RAY DIFFRACTION99
2.9761-3.11150.24781370.22622546X-RAY DIFFRACTION98
3.1115-3.27550.2851350.21952536X-RAY DIFFRACTION98
3.2755-3.48060.27961330.20862538X-RAY DIFFRACTION99
3.4806-3.74910.27881370.20932547X-RAY DIFFRACTION98
3.7491-4.1260.21871360.1932565X-RAY DIFFRACTION99
4.126-4.72220.20721330.15612568X-RAY DIFFRACTION98
4.7222-5.94620.20131340.17762588X-RAY DIFFRACTION98
5.9462-39.28590.24391470.2032593X-RAY DIFFRACTION95
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)
17.35020.4039-1.34863.6581-0.10128.8514-0.23580.79060.1699-0.36460.0801-0.3286-0.8796-0.33790.12470.48930.05880.08560.66330.08260.497614.934820.6609-8.4813
23.4465-0.2493-1.6742.0380.25747.64270.07470.25220.65840.0719-0.0286-0.2821-0.72250.4282-0.03340.63320.0705-0.03570.38570.1530.66817.775523.3378-1.34
30.87820.5926-0.85625.5785-2.89594.24170.07430.09970.10710.3223-0.3398-0.1628-0.43740.11910.25460.33260.0515-0.05210.4007-0.06940.489111.67565.599911.682
41.31820.7849-0.8226.5054-1.51834.1510.10330.0486-0.22690.6425-0.28130.08830.3908-0.27320.10150.4391-0.02670.00970.387-0.09580.49523.8872-11.037825.8458
50.59990.7907-0.72952.187-2.68138.7392-0.10260.03940.03940.2477-0.0669-0.0582-0.4329-0.30880.17610.28550.0759-0.00220.3083-0.11840.49355.08530.029720.1247
64.52930.9291-2.9654.84530.60916.44580.05990.55990.178-0.501-0.2341-0.4131-0.41760.76520.33180.42470.06030.12490.2278-0.09150.540411.1719-4.57099.2701
72.0231.62982.18532.05580.83619.3727-0.27031.304-1.90410.25060.08380.47010.9928-1.4355-0.0830.7214-0.35450.00181.1622-0.19440.6733-20.9955-14.8289-6.7479
86.05541.3494.34561.89210.24446.9657-0.09970.8377-0.206-0.26540.16450.1060.2557-0.852-0.10130.3892-0.04510.0331.0578-0.09630.4728-13.2816-5.267-3.8382
95.35662.01344.70121.3631.77144.3145-0.52321.1875-0.297-0.190.2035-0.06241.0895-1.695-0.0780.3222-0.1684-0.11881.8865-0.15210.4886-20.7297-8.8197-3.3694
104.1362.2796.35593.5132.87484.95090.251-0.6158-0.8053-0.2310.101-0.07110.8311-0.7016-0.26860.7132-0.24460.04861.1385-0.13450.6402-15.51-14.7965-13.6196
119.0664-4.16580.55462.1184-3.02368.04120.6496-2.1022-1.80010.3449-0.22720.18860.7795-0.3906-0.57760.9554-0.4903-0.07751.3631-0.00760.9885-25.6377-27.5932-24.4263
122.0503-8.2978-1.76811.99842.31999.50.41630.1874-3.2930.648-0.65340.62813.00552.38050.17481.74540.3637-0.16451.37740.07081.5043-14.3784-33.9784-27.7746
136.52561.35131.53279.12745.67269.1280.5002-0.1877-1.0557-0.28280.05890.21591.07160.2883-0.50560.9811-0.2056-0.00250.7518-0.09660.8944-24.3609-26.8788-30.0581
142.29986.80569.42827.20481.42941.99571.6624-1.0689-1.60171.9199-0.1789-0.87122.5353-0.817-1.36361.2903-0.233-0.08161.12360.02231.1955-26.4262-34.13-20.9416
152.13971.0619-1.11955.08970.47386.8515-0.38490.8705-0.2743-1.1240.5156-0.54180.2021-0.2453-0.1720.6923-0.12730.17521.2071-0.22670.5498-0.4952-2.7111-22.8464
166.8582.46430.58838.04431.24936.7569-0.47250.9992-0.3996-0.84850.3888-0.09030.8053-0.78210.08650.6817-0.15870.13841.1385-0.10550.4736-4.2124-4.1952-21.3073
174.60665.72397.55932.08059.28932.072-0.09640.5331-1.2902-1.42040.0155-0.7929-0.3948-1.48060.10221.6751-0.2440.21491.7821-0.24910.7628-6.3708-17.2767-40.1424
184.1862-4.5522-1.75.23981.46756.8541.8367-0.5501-4.1686-0.06460.1821-0.10780.24050.2732-1.2491.9762-0.8206-0.35581.7842-0.86421.4843-31.5088-31.4066-37.2354
192.12936.8266-0.35926.4722-0.11860.2085-0.83722.3682-0.6093-0.52830.3789-0.11920.2651-0.84610.42921.2025-0.26640.15131.3595-0.310.8063-19.9694-21.1607-40.3132
202.08862.70286.58257.8056-1.56097.7063-0.45154.38640.68740.39750.70091.05090.21030.4088-0.50141.1279-0.29340.03011.4477-0.02120.8207-29.7127-18.4873-39.4725
211.9878-5.45652.61852.0259-1.21092.0303-1.1933-1.20590.3808-0.39182.6738-2.39770.16692.0553-1.63831.1107-0.08050.03421.3199-0.45521.0941-9.385-21.3062-34.3994
221.98828.57751.92489.7057-6.32439.4997-0.52782.9374-0.24780.31881.4460.636-0.2205-1.1204-0.73581.0171-0.0207-0.18681.0592-0.17680.985-37.2558-24.4435-39.2097
232.00041.99951.999921.99982.0003-1.911-26.85354.25279.4686-0.6977-3.9001-2.291-2.21992.53360.91770.3063-0.08541.9981-0.23470.9084-3.65283.9578-6.3129
243.4943-1.341-3.84918.46836.53613.0384-0.16270.61860.00590.5524-0.39720.09460.0306-0.11370.550.76860.2873-0.1290.80340.13370.48546.459421.3351-5.0694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 6:52 )A6 - 52
2X-RAY DIFFRACTION2( CHAIN A AND RESID 53:117 )A53 - 117
3X-RAY DIFFRACTION3( CHAIN A AND RESID 118:213 )A118 - 213
4X-RAY DIFFRACTION4( CHAIN A AND RESID 214:274 )A214 - 274
5X-RAY DIFFRACTION5( CHAIN A AND RESID 275:342 )A275 - 342
6X-RAY DIFFRACTION6( CHAIN A AND RESID 343:361 )A343 - 361
7X-RAY DIFFRACTION7( CHAIN H AND RESID 5:20 )H5 - 20
8X-RAY DIFFRACTION8( CHAIN H AND RESID 21:76 )H21 - 76
9X-RAY DIFFRACTION9( CHAIN H AND RESID 77:94 )H77 - 94
10X-RAY DIFFRACTION10( CHAIN H AND RESID 95:146 )H95 - 146
11X-RAY DIFFRACTION11( CHAIN H AND RESID 147:164 )H147 - 164
12X-RAY DIFFRACTION12( CHAIN H AND RESID 165:175 )H165 - 175
13X-RAY DIFFRACTION13( CHAIN H AND RESID 176:204 )H176 - 204
14X-RAY DIFFRACTION14( CHAIN H AND RESID 205:223 )H205 - 223
15X-RAY DIFFRACTION15( CHAIN L AND RESID 1:76 )L1 - 76
16X-RAY DIFFRACTION16( CHAIN L AND RESID 77:103 )L77 - 103
17X-RAY DIFFRACTION17( CHAIN L AND RESID 104:114 )L104 - 114
18X-RAY DIFFRACTION18( CHAIN L AND RESID 115:129 )L115 - 129
19X-RAY DIFFRACTION19( CHAIN L AND RESID 130:148 )L130 - 148
20X-RAY DIFFRACTION20( CHAIN L AND RESID 149:164 )L149 - 164
21X-RAY DIFFRACTION21( CHAIN L AND RESID 165:175 )L165 - 175
22X-RAY DIFFRACTION22( CHAIN L AND RESID 176:190 )L176 - 190
23X-RAY DIFFRACTION23( CHAIN L AND RESID 303:303 )L303
24X-RAY DIFFRACTION24( CHAIN V AND RESID 346:368 )V346 - 368

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Yorodumi

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  • 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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