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- PDB-5dh9: Crystal Structure of PKI NES Flip Mutant Peptide in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5dh9
TitleCrystal Structure of PKI NES Flip Mutant Peptide in complex with CRM1-Ran-RanBP1
Components
  • Engineered Nuclear Export Signal Peptide (PKINES-Flip3 mutant)
  • Exportin-1
  • GTP-binding nuclear protein Ran
  • Ran-specific GTPase-activating protein 1
KeywordsTRANSPORT PROTEIN / Peptides / HEAT repeat / Nuclear Export signal / Exportin-1 / Nuclear Transport
Function / homology
Function and homology information


Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA re-export from nucleus / negative regulation of cAMP-dependent protein kinase activity / negative regulation of cAMP/PKA signal transduction / RNA nuclear export complex / pre-miRNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear export signal receptor activity / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response ...Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA re-export from nucleus / negative regulation of cAMP-dependent protein kinase activity / negative regulation of cAMP/PKA signal transduction / RNA nuclear export complex / pre-miRNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear export signal receptor activity / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / manchette / cellular response to mineralocorticoid stimulus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / tRNA export from nucleus / SUMOylation of SUMOylation proteins / importin-alpha family protein binding / protein localization to kinetochore / SUMOylation of RNA binding proteins / protein localization to nucleolus / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / nuclear export / RNA export from nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of chromatin organization proteins / cAMP-dependent protein kinase inhibitor activity / spindle pole body / MicroRNA (miRNA) biogenesis / nuclear import signal receptor activity / DNA metabolic process / dynein intermediate chain binding / negative regulation of protein import into nucleus / NLS-bearing protein import into nucleus / MAPK6/MAPK4 signaling / protein kinase A catalytic subunit binding / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / U5 snRNA binding / viral process / mRNA export from nucleus / U2 snRNA binding / U6 snRNA binding / nuclear pore / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / U1 snRNA binding / regulation of G2/M transition of mitotic cell cycle / protein export from nucleus / centriole / GTPase activator activity / mitotic spindle organization / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / recycling endosome / G protein activity / kinetochore / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / G1/S transition of mitotic cell cycle / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / midbody / actin cytoskeleton organization / ubiquitin-dependent protein catabolic process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / chromatin / nucleolus / GTP binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Ran-specific GTPase-activating protein 1, Ran-binding domain / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / CRM1 C terminal ...Ran-specific GTPase-activating protein 1, Ran-binding domain / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / Ran binding domain / Ran binding protein RanBP1-like / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / small GTPase Ran family profile. / Ran GTPase / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / PH-like domain superfamily / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Exportin-1 / Ran-specific GTPase-activating protein 1 / cAMP-dependent protein kinase inhibitor alpha / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsFung, H.Y. / Chook, Y.M.
Funding support Hong Kong, United States, 6items
OrganizationGrant numberCountry
Croucher FoundationStudent Scholarship Hong Kong
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069909 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP120352 United States
University of Texas SouthwesternEndowed Scholars Program United States
Welch FoundationI-1532 United States
Leukemia & Lymphoma SocietyScholar Award United States
CitationJournal: Elife / Year: 2015
Title: Structural determinants of nuclear export signal orientation in binding to exportin CRM1.
Authors: Fung, H.Y. / Fu, S.C. / Brautigam, C.A. / Chook, Y.M.
History
DepositionAug 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 24, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-binding nuclear protein Ran
B: Ran-specific GTPase-activating protein 1
C: Exportin-1
D: Engineered Nuclear Export Signal Peptide (PKINES-Flip3 mutant)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,7219
Polymers162,8994
Non-polymers8235
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11130 Å2
ΔGint-56 kcal/mol
Surface area57390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.118, 106.118, 304.127
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 26758.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL219(DE3) / References: UniProt: P62826
#2: Protein Ran-specific GTPase-activating protein 1 / Chromosome stability protein 20 / Perinuclear array-localized protein / Ran-binding protein 1 / RANBP1


Mass: 16521.867 Da / Num. of mol.: 1 / Fragment: RanDB1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Plasmid: pGex4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL219(DE3) / References: UniProt: P41920
#3: Protein Exportin-1 / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 117458.781 Da / Num. of mol.: 1 / Mutation: V441D,D536G,T539C,V540E,K541Q,Y1022C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Plasmid: pGex4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL219(DE3) / References: UniProt: P30822

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Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide Engineered Nuclear Export Signal Peptide (PKINES-Flip3 mutant)


Mass: 2159.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKIA / Plasmid: pMal / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61925*PLUS

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Non-polymers , 4 types, 258 molecules

#5: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 17% PEG3350, 100mM Bis-Tris pH6.4, 200mM NH4NO3, 10mM Spermine HCl

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2015
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 58218 / % possible obs: 99.6 % / Redundancy: 5.5 % / Biso Wilson estimate: 34.85 Å2 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.041 / Rrim(I) all: 0.089 / Χ2: 0.918 / Net I/av σ(I): 18.989 / Net I/σ(I): 7.3 / Num. measured all: 320312
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.55-2.595.50.98728800.6690.4650.888100
2.59-2.645.50.90628450.7010.4240.909100
2.64-2.695.60.8128760.7180.3790.9251000.896
2.69-2.755.60.67528770.80.3140.9541000.746
2.75-2.815.60.58628730.8370.2720.9411000.648
2.81-2.875.60.47328510.90.2190.98299.90.523
2.87-2.945.60.41228690.9150.1920.96699.90.456
2.94-3.025.60.33928860.9320.1570.97299.90.375
3.02-3.115.60.26428700.9490.1230.9581000.292
3.11-3.215.60.21129110.9660.0990.961000.234
3.21-3.335.60.1628800.9770.0740.94399.90.177
3.33-3.465.60.12529000.9860.0590.94799.90.139
3.46-3.625.50.09828970.9890.0460.93399.90.108
3.62-3.815.50.07829240.9930.0360.92199.90.086
3.81-4.055.50.06229200.9950.0280.87399.80.068
4.05-4.365.50.05329160.9960.0240.89699.60.058
4.36-4.85.50.0529380.9950.0231.08299.30.055
4.8-5.495.40.04929650.9950.0221.0399.20.054
5.49-6.925.20.0429990.9970.0180.66998.70.044
6.92-5050.02531410.9980.0120.58796.70.028

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HB2

4hb2


Resolution: 2.55→47.457 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 22.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 1998 3.51 %Random selection
Rwork0.1862 54864 --
obs0.1876 56862 97.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.83 Å2 / Biso mean: 46.7496 Å2 / Biso min: 12.32 Å2
Refinement stepCycle: final / Resolution: 2.55→47.457 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10820 0 51 253 11124
Biso mean--40.27 35.29 -
Num. residues----1341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411181
X-RAY DIFFRACTIONf_angle_d0.67315134
X-RAY DIFFRACTIONf_chiral_restr0.0261723
X-RAY DIFFRACTIONf_plane_restr0.0031921
X-RAY DIFFRACTIONf_dihedral_angle_d12.4694181
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5387-2.60210.30561220.24993361348385
2.6021-2.67250.27581380.23983766390496
2.6725-2.75110.3221370.23763779391696
2.7511-2.83990.28471380.23613789392796
2.8399-2.94140.26721420.22883873401597
2.9414-3.05920.28161430.23073919406299
3.0592-3.19830.29411440.224339564100100
3.1983-3.36690.25411440.205839764120100
3.3669-3.57780.21681470.198640254172100
3.5778-3.85390.20581460.17440054151100
3.8539-4.24160.19441480.15940464194100
4.2416-4.85480.19091470.13744043419099
4.8548-6.11450.19461490.16554084423399
6.1145-47.46570.18061530.15484242439597
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)
13.3456-0.5620.81330.4121-1.21063.92210.03870.1727-0.4477-0.32760.2715-0.8236-0.26760.4876-0.27660.2011-0.05850.03820.2613-0.07410.4357.795344.296337.8828
22.0581-1.0458-0.79221.90410.74442.830.08430.2945-0.0387-0.27990.308-0.5901-0.65770.5425-0.33090.235-0.1250.10230.3883-0.13170.51229.373449.592931.6815
32.6208-0.8423-0.53921.0894-0.20481.53810.01330.042-0.31330.11380.0883-0.46910.19990.21-0.06610.18510.009-0.0410.3375-0.09810.53757.942237.030437.2284
42.4647-0.3726-0.75584.7388-1.46243.47320.10540.2452-0.2234-0.289-0.0039-0.13480.45020.0983-0.05610.09780.02270.03960.2107-0.07110.2839-3.447638.354336.8135
52.09370.7607-1.49214.2717-2.94676.9419-0.0155-0.05230.1571-0.27220.0517-0.0643-0.1112-0.2049-0.16050.20530.0543-0.02390.2504-0.08020.2775-7.076746.370337.6451
65.24580.7974-0.11426.64890.90044.36360.0718-0.25690.2565-0.05670.0498-0.1217-0.92980.201-0.13310.3561-0.0203-0.01210.2566-0.06380.26121.81654.190343.77
71.39832.3668-1.86773.9596-3.55545.08060.58150.10430.56360.71350.0570.3832-1.70960.532-0.75030.6606-0.1585-0.01890.5743-0.01970.5329.422967.637234.6346
80.1635-0.06720.16120.6627-0.55280.53340.3268-0.41870.0754-0.83610.2184-0.902-0.31860.5679-0.50170.6408-0.22020.24130.9773-0.35770.720218.540762.27384.6863
95.2887-1.52661.20375.01493.35978.3049-0.1268-0.1296-0.37310.62710.10990.53520.8108-0.72690.15540.4104-0.10690.09570.4337-0.03940.6637-1.6455.992612.02
101.2937-0.1998-1.11920.53840.30572.50780.7098-0.51680.1823-0.04470.0314-0.4176-1.61580.5303-0.68281.0767-0.33890.01420.61410.01730.78352.526482.006248.8098
115.1611-0.64650.46315.84070.19263.2360.0519-0.0072-0.44480.4288-0.0950.6058-0.24310.5114-0.01440.4242-0.17370.15930.43910.01720.42497.002862.689717.2923
120.6904-0.0442-0.2862.8834-1.62481.073-0.286-0.14450.05440.10160.06730.0837-0.85190.52040.21250.7904-0.3110.17820.521-0.01480.55567.236272.397924.5285
132.07742.1375-0.03614.43131.37470.9139-0.22180.0660.1037-0.57940.12380.0613-0.92070.51280.14920.6958-0.2660.11350.4951-0.00220.47237.491670.387712.2252
141.6864-0.433-0.12392.00480.54221.4814-0.0561-0.23480.03070.59550.2244-0.70830.37410.3941-0.01020.24680.1091-0.20460.3578-0.06060.56697.965725.543153.6463
151.9486-0.7740.68742.2777-0.56683.74750.03420.0471-0.03040.10470.07020.0338-0.1036-0.2535-0.10470.19220.00180.00170.2567-0.07850.1805-24.082748.598254.1365
160.81760.09930.65010.93760.02723.60170.2608-0.10720.2717-0.27670.0381-0.0458-1.8942-1.0851-0.03910.72220.42330.13590.60980.1160.3284-33.312864.02319.0638
171.3849-1.39330.30312.5851-0.23011.510.01530.1589-0.0975-0.04170.1350.0601-0.1334-0.0481-0.15710.21780.00350.05430.3252-0.02260.2105-15.829139.25640.8685
181.4393-0.7971.52721.613-1.16643.87250.19250.0083-0.4049-0.15770.08640.29670.321-0.1171-0.2340.1777-0.00630.01010.2583-0.04560.4168-7.06510.239420.582
195.5681-0.93372.12964.09981.61461.8053-0.29420.17530.9324-0.50.22330.1509-1.009-0.57260.09921.7020.709-0.07530.9718-0.02670.5622-39.570375.326327.5861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 22 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 66 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 91 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 132 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 133 through 158 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 159 through 169 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 170 through 190 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 191 through 206 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 207 through 216 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 64 through 82 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 83 through 106 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 107 through 139 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 140 through 200 )B0
14X-RAY DIFFRACTION14chain 'C' and (resid 0 through 268 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 269 through 495 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 496 through 692 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 693 through 897 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 898 through 1052 )C0
19X-RAY DIFFRACTION19chain 'D' and (resid 6 through 19 )D0

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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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