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- PDB-8tzx: Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and ... -

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Open data


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Basic information

Entry
Database: PDB / ID: 8tzx
TitleTernary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue dWIZ-1
Components
  • DNA damage-binding protein 1
  • Protein Wiz
  • Protein cereblon
KeywordsLIGASE / Complex / glue
Function / homology
Function and homology information


positive regulation of nuclear cell cycle DNA replication / negative regulation of monoatomic ion transmembrane transport / histone methyltransferase binding / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition ...positive regulation of nuclear cell cycle DNA replication / negative regulation of monoatomic ion transmembrane transport / histone methyltransferase binding / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / locomotory exploration behavior / cullin family protein binding / viral release from host cell / positive regulation of Wnt signaling pathway / ectopic germ cell programmed cell death / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / proteasomal protein catabolic process / positive regulation of gluconeogenesis / transcription corepressor binding / nucleotide-excision repair / positive regulation of protein-containing complex assembly / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / positive regulation of protein catabolic process / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / rhythmic process / site of double-strand break / Neddylation / midbody / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / transmembrane transporter binding / damaged DNA binding / chromosome, telomeric region / DNA-binding transcription factor activity, RNA polymerase II-specific / protein stabilization / protein ubiquitination / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA repair / apoptotic process / DNA damage response / regulation of transcription by RNA polymerase II / protein-containing complex binding / negative regulation of apoptotic process / nucleolus / perinuclear region of cytoplasm / protein-containing complex / DNA binding / extracellular space / extracellular exosome / zinc ion binding / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / : / Zinc finger found in WIZ protein / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily ...: / : / Zinc finger found in WIZ protein / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / PUA-like superfamily / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / Protein Wiz / DNA damage-binding protein 1 / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsClifton, M.C. / Ma, X. / Ornelas, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Science / Year: 2024
Title: A molecular glue degrader of the WIZ transcription factor for fetal hemoglobin induction.
Authors: Ting, P.Y. / Borikar, S. / Kerrigan, J.R. / Thomsen, N.M. / Aghania, E. / Hinman, A.E. / Reyes, A. / Pizzato, N. / Fodor, B.D. / Wu, F. / Belew, M.S. / Mao, X. / Wang, J. / Chitnis, S. / ...Authors: Ting, P.Y. / Borikar, S. / Kerrigan, J.R. / Thomsen, N.M. / Aghania, E. / Hinman, A.E. / Reyes, A. / Pizzato, N. / Fodor, B.D. / Wu, F. / Belew, M.S. / Mao, X. / Wang, J. / Chitnis, S. / Niu, W. / Hachey, A. / Cobb, J.S. / Savage, N.A. / Burke, A. / Paulk, J. / Dovala, D. / Lin, J. / Clifton, M.C. / Ornelas, E. / Ma, X. / Ware, N.F. / Sanchez, C.C. / Taraszka, J. / Terranova, R. / Knehr, J. / Altorfer, M. / Barnes, S.W. / Beckwith, R.E.J. / Solomon, J.M. / Dales, N.A. / Patterson, A.W. / Wagner, J. / Bouwmeester, T. / Dranoff, G. / Stevenson, S.C. / Bradner, J.E.
History
DepositionAug 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein cereblon
B: DNA damage-binding protein 1
C: Protein Wiz
D: Protein cereblon
E: DNA damage-binding protein 1
F: Protein Wiz
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,74417
Polymers279,2376
Non-polymers1,50711
Water21612
1
A: Protein cereblon
B: DNA damage-binding protein 1
C: Protein Wiz
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,4039
Polymers139,6183
Non-polymers7846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Protein cereblon
E: DNA damage-binding protein 1
F: Protein Wiz
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,3418
Polymers139,6183
Non-polymers7225
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.669, 137.742, 136.628
Angle α, β, γ (deg.)90.00, 96.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein Protein cereblon


Mass: 42971.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96SW2
#2: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 93347.078 Da / Num. of mol.: 2
Fragment: UNP residues 1-395,706-1140,UNP residues 1-395,706-1140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide Protein Wiz / Widely-interspaced zinc finger-containing protein / Zinc finger protein 803


Mass: 3299.722 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WIZ, ZNF803 / Production host: Escherichia coli (E. coli) / References: UniProt: O95785

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Non-polymers , 5 types, 23 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-U3I / (3S)-3-(5-{(1R)-1-[(2R)-1-ethylpiperidin-2-yl]ethoxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione


Mass: 399.483 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H29N3O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→39.39 Å / Num. obs: 48824 / % possible obs: 100 % / Redundancy: 13.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.05617 / Rpim(I) all: 0.074 / Rrim(I) all: 0.275 / Χ2: 1.01 / Net I/σ(I): 7.2 / Num. measured all: 677068
Reflection shellResolution: 3.15→3.25 Å / % possible obs: 100 % / Redundancy: 13.9 % / Rmerge(I) obs: 1.028 / Num. measured all: 62023 / Num. unique obs: 4468 / CC1/2: 0.38 / Rpim(I) all: 1.325 / Rrim(I) all: 4.948 / Χ2: 1.05 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
pointlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→39.31 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2519 2501 5.13 %
Rwork0.2133 --
obs0.2152 48743 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→39.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16913 0 86 12 17011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00217335
X-RAY DIFFRACTIONf_angle_d0.51823672
X-RAY DIFFRACTIONf_dihedral_angle_d6.8432438
X-RAY DIFFRACTIONf_chiral_restr0.0432788
X-RAY DIFFRACTIONf_plane_restr0.0033057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.210.49081320.41162572X-RAY DIFFRACTION99
3.21-3.280.38781240.36362561X-RAY DIFFRACTION100
3.28-3.350.36551580.31752538X-RAY DIFFRACTION100
3.35-3.430.32631430.29662532X-RAY DIFFRACTION100
3.43-3.510.29711440.28142568X-RAY DIFFRACTION100
3.51-3.610.30311500.26212520X-RAY DIFFRACTION100
3.61-3.710.28811750.25382535X-RAY DIFFRACTION100
3.71-3.830.27771380.24362581X-RAY DIFFRACTION100
3.83-3.970.28061260.22142558X-RAY DIFFRACTION100
3.97-4.130.26341100.21262592X-RAY DIFFRACTION100
4.13-4.310.25891060.19362599X-RAY DIFFRACTION100
4.31-4.540.21011440.18152567X-RAY DIFFRACTION100
4.54-4.830.20631690.17052540X-RAY DIFFRACTION100
4.83-5.20.22171580.1862538X-RAY DIFFRACTION100
5.2-5.720.22971420.20042594X-RAY DIFFRACTION100
5.72-6.540.26331330.21822585X-RAY DIFFRACTION100
6.54-8.230.25081290.2162603X-RAY DIFFRACTION100
8.23-39.310.20951200.17762659X-RAY DIFFRACTION100
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)
11.51931.69310.35043.75950.83842.5144-0.4909-0.0206-0.3202-0.41120.50320.0403-0.24520.22920.16141.12520.0725-0.10980.8989-0.09291.1334-22.473917.82747.3906
21.1293-0.41671.11662.30161.13713.2651-0.3238-0.35210.38960.407-0.0072-0.0142-0.2546-0.42190.33620.99270.1421-0.13860.9265-0.11830.8103-31.47739.357623.1457
322.00011.99991.9998-2.63521.9999-0.53392.69-0.17820.02870.4299-0.49380.5275-1.3586-0.00852.195-0.1103-0.32521.97740.53671.8823-25.3057-9.337930.4163
42.07660.5248-0.19912.7385-0.321.8972-0.11890.1774-0.0354-0.29750.11850.37810.1708-0.10730.04150.81940.0393-0.05290.6858-0.13080.8151-51.1198-9.2603-26.2644
54.03360.3662-0.07634.3126-0.06882.65970.1856-0.08810.2123-0.1415-0.1382-0.1398-0.5048-0.1637-0.05120.72450.039-0.02770.6895-0.06720.6875-51.936410.2047-21.5716
64.16720.1075-0.91093.9149-0.18943.67240.03620.01350.5770.34840.35610.28750.1101-0.7742-0.42410.80990.06620.06131.003-0.07670.8808-68.68896.5087-9.2629
72.7281-1.4211-0.06362.2235-0.94520.96180.19310.1117-0.2658-0.19040.06270.28440.3152-0.4621-0.17650.8983-0.0427-0.09620.9605-0.12090.9765-67.771-9.8169-14.0754
82.83831.47790.57171.0016-0.84315.1437-0.059-0.1942-0.1733-0.0320.1228-0.06090.9928-0.33070.13281.1826-0.0996-0.27330.69920.00050.9862-48.5363-28.371-3.4523
92.47940.22490.89833.3999-0.40732.57440.1109-0.5215-0.28510.7857-0.1917-0.2390.0868-0.02180.08461.1456-0.1011-0.00571.02360.13940.9309-49.5826-24.598212.4323
102.0070.14890.47572.482-0.94032.53380.2015-0.427-0.35890.5085-0.1777-0.52570.06590.4674-0.02420.99940.0428-0.20580.911-0.03260.9895-28.5818-18.99292.5704
114.3134-0.02930.40123.7306-0.20222.85140.3790.3987-0.5855-0.0878-0.0261-0.0840.38950.0423-0.34990.86920.0689-0.03050.9023-0.13390.9768-28.3354-14.989-28.1233
123.5117-1.1491.35374.2939-1.1233.5093-0.3509-0.285-0.1294-0.76560.51910.451-0.3136-0.53890.26781.34410.0789-0.43210.7217-0.0381.0573-9.527723.420839.6932
136.8043-1.8064-1.42624.5354-2.37222.8551-0.52810.7704-0.5287-0.0566-0.1209-0.82660.358-0.34360.52641.16960.0034-0.0311.0415-0.00311.0291-4.965516.973537.031
142.6478-0.5773-2.17854.5985-0.79697.315-0.34820.6083-0.4437-1.66130.4540.09191.11980.4595-0.20821.4174-0.0219-0.0340.9089-0.16841.1192-38.2287-4.6891-95.2835
156.04370.42951.44044.9817-2.31235.50480.3176-0.5304-0.4795-2.69570.1054-0.0695-0.27230.0522-0.14491.70470.06950.0630.6333-0.09090.7129-36.3423-0.2903-91.5816
164.5287-1.366-1.31391.2159-1.21273.57690.43670.2391-0.7482-1.10320.34110.2908-0.14410.1265-0.73681.93810.029-0.18240.7246-0.05461.0013-38.6123-7.7158-94.0447
171.3444-0.24490.96612.87262.4592.972-0.19590.5467-0.3506-0.87620.5131-1.2006-1.02540.1935-0.01571.6326-0.10.24091.0809-0.12430.9684-30.33876.3912-90.3544
183.01211.23441.58722.59741.32586.10420.4103-0.5638-0.18540.2265-0.13640.0020.4955-0.5271-0.28940.81030.0176-0.01360.77450.00950.7577-39.88749.6643-65.1695
192.7161.17281.70222.314-0.68193.95580.417-0.1126-0.2349-0.2676-0.35270.35850.63420.0223-0.11911.1030.0447-0.26370.9012-0.12690.8811-63.4026-0.4282-81.83
201.15770.2447-1.58582.9342-0.83431.9878-0.0340.07360.0922-0.20290.1951-0.80040.09760.7873-0.14630.67470.1353-0.00511.2679-0.25861.0464-6.205610.3427-54.9205
210.38671.24910.65624.79060.36465.1415-0.9324-0.53370.31570.22061.2404-0.54640.99441.3243-0.23210.67840.18160.02611.2318-0.18930.9055-17.6868-1.8943-39.6892
220.5078-0.0395-0.59193.6291-1.81573.09810.0513-0.1835-0.01310.4790.0964-0.3749-0.18140.4112-0.06910.76050.0179-0.01651.2246-0.21740.9379-16.545417.0476-36.306
232.98480.11-0.63121.99690.47012.29140.31280.11920.3126-0.447-0.04280.0673-0.52240.0516-0.27640.8212-0.01560.13120.6281-0.01960.8078-35.8135.1327-61.1967
241.527-2.03910.02683.04020.60553.4553-0.076-0.85240.6631-0.25670.1665-0.8248-0.18840.6623-0.29421.0239-0.27270.41091.5364-0.11471.392-3.801931.6076-73.7449
258.62820.91475.57951.3486-0.38954.44521.1045-0.1379-0.3378-0.628-0.04860.49880.5467-1.0366-0.90621.34360.0121-0.44281.33260.0761.1534-67.3877-7.8799-98.0987
268.36480.09432.13535.5109-1.07897.93520.39420.33940.2933-0.668-0.05240.61340.13270.3318-0.31041.11360.1123-0.02421.1378-0.10831.0875-65.0618-0.4337-101.1286
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 77 through 206 )
2X-RAY DIFFRACTION2chain 'A' and (resid 207 through 427 )
3X-RAY DIFFRACTION3chain 'A' and (resid 428 through 428 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 84 )
5X-RAY DIFFRACTION5chain 'B' and (resid 85 through 204 )
6X-RAY DIFFRACTION6chain 'B' and (resid 205 through 263 )
7X-RAY DIFFRACTION7chain 'B' and (resid 264 through 365 )
8X-RAY DIFFRACTION8chain 'B' and (resid 366 through 743 )
9X-RAY DIFFRACTION9chain 'B' and (resid 744 through 851 )
10X-RAY DIFFRACTION10chain 'B' and (resid 852 through 1044 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1045 through 1140 )
12X-RAY DIFFRACTION12chain 'C' and (resid 868 through 881 )
13X-RAY DIFFRACTION13chain 'C' and (resid 882 through 893 )
14X-RAY DIFFRACTION14chain 'D' and (resid 76 through 115 )
15X-RAY DIFFRACTION15chain 'D' and (resid 116 through 143 )
16X-RAY DIFFRACTION16chain 'D' and (resid 144 through 170 )
17X-RAY DIFFRACTION17chain 'D' and (resid 171 through 192 )
18X-RAY DIFFRACTION18chain 'D' and (resid 193 through 317 )
19X-RAY DIFFRACTION19chain 'D' and (resid 318 through 427 )
20X-RAY DIFFRACTION20chain 'E' and (resid 2 through 204 )
21X-RAY DIFFRACTION21chain 'E' and (resid 205 through 244 )
22X-RAY DIFFRACTION22chain 'E' and (resid 245 through 365 )
23X-RAY DIFFRACTION23chain 'E' and (resid 366 through 1044 )
24X-RAY DIFFRACTION24chain 'E' and (resid 1045 through 1140 )
25X-RAY DIFFRACTION25chain 'F' and (resid 868 through 881 )
26X-RAY DIFFRACTION26chain 'F' and (resid 882 through 893 )

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Jul 12, 2017. Major update of PDB

Major update of PDB

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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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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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