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- PDB-7eaa: crystal structure of NDP52 SKICH domain in complex with RB1CC1 co... -

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Basic information

Entry
Database: PDB / ID: 7eaa
Titlecrystal structure of NDP52 SKICH domain in complex with RB1CC1 coiled-coil domain
Components
  • Calcium-binding and coiled-coil domain-containing protein 2
  • RB1-inducible coiled-coil protein 1
KeywordsPROTEIN BINDING / NDP52 SKICH / complex / RB1CC1 coiled-coil
Function / homology
Function and homology information


regulation of protein lipidation / ribophagy / glycophagy / Atg1/ULK1 kinase complex / xenophagy / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / reticulophagy / positive regulation of autophagosome maturation ...regulation of protein lipidation / ribophagy / glycophagy / Atg1/ULK1 kinase complex / xenophagy / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / reticulophagy / positive regulation of autophagosome maturation / Macroautophagy / response to type II interferon / autophagosome membrane / positive regulation of cell size / autophagosome assembly / autophagosome / positive regulation of autophagy / extrinsic apoptotic signaling pathway / protein-membrane adaptor activity / viral process / liver development / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / PML body / autophagy / heart development / cytoplasmic vesicle / nuclear membrane / molecular adaptor activity / lysosome / cytoskeleton / positive regulation of protein phosphorylation / cell cycle / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / protein kinase binding / perinuclear region of cytoplasm / protein homodimerization activity / membrane / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11 / SKICH domain / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile.
Similarity search - Domain/homology
Calcium-binding and coiled-coil domain-containing protein 2 / RB1-inducible coiled-coil protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFu, T. / Pan, L.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21672253 China
National Natural Science Foundation of China (NSFC)21822705 China
National Natural Science Foundation of China (NSFC)21621002 China
CitationJournal: Sci Adv / Year: 2021
Title: Structural and biochemical advances on the recruitment of the autophagy-initiating ULK and TBK1 complexes by autophagy receptor NDP52.
Authors: Fu, T. / Zhang, M. / Zhou, Z. / Wu, P. / Peng, C. / Wang, Y. / Gong, X. / Li, Y. / Wang, Y. / Xu, X. / Li, M. / Shen, L. / Pan, L.
History
DepositionMar 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: RB1-inducible coiled-coil protein 1
D: RB1-inducible coiled-coil protein 1
B: Calcium-binding and coiled-coil domain-containing protein 2
A: Calcium-binding and coiled-coil domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)59,0684
Polymers59,0684
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9180 Å2
ΔGint-57 kcal/mol
Surface area25960 Å2
Unit cell
Length a, b, c (Å)69.439, 69.439, 246.095
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein RB1-inducible coiled-coil protein 1 / FAK family kinase-interacting protein of 200 kDa / FIP200


Mass: 13565.216 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RB1CC1, KIAA0203, RBICC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8TDY2
#2: Protein Calcium-binding and coiled-coil domain-containing protein 2 / Antigen nuclear dot 52 kDa protein / Nuclear domain 10 protein NDP52 / Nuclear domain 10 protein 52 ...Antigen nuclear dot 52 kDa protein / Nuclear domain 10 protein NDP52 / Nuclear domain 10 protein 52 / Nuclear dot protein 52


Mass: 15968.882 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALCOCO2, NDP52 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13137
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MgCl2, 0.1 M MES pH 6.0, 8% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 19751 / % possible obs: 99.7 % / Redundancy: 17.3 % / Biso Wilson estimate: 35.01 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 23.65
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 2.815 / Num. unique obs: 1942

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z7A

5z7a


Resolution: 2.6→46.05 Å / SU ML: 0.2967 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.8343
RfactorNum. reflection% reflection
Rfree0.2534 915 4.92 %
Rwork0.199 17698 -
obs0.2017 18613 94.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.6 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3690 0 0 67 3757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00853757
X-RAY DIFFRACTIONf_angle_d0.91015042
X-RAY DIFFRACTIONf_chiral_restr0.051534
X-RAY DIFFRACTIONf_plane_restr0.0047654
X-RAY DIFFRACTIONf_dihedral_angle_d10.4122301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.720.3521870.25761616X-RAY DIFFRACTION62.2
2.72-2.890.31911200.23942589X-RAY DIFFRACTION97.73
2.89-3.120.3341520.22722584X-RAY DIFFRACTION99.93
3.12-3.430.27831310.2012651X-RAY DIFFRACTION99.86
3.43-3.930.21171430.18022672X-RAY DIFFRACTION99.93
3.93-4.950.19991340.16452719X-RAY DIFFRACTION99.76
4.95-46.050.24711480.20882867X-RAY DIFFRACTION99.21
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)
10.2954800583910.2866335052640.7758746790231.355928039422.210260474194.49936840875-0.413323581711-0.03338471936550.118919890097-0.325257451654-0.208958634520.313142348646-0.4687110921060.07022925677440.4631066401210.18826741127-0.06674446020810.05793151716880.298072518878-0.08152199810460.221192823998-13.552214631113.8962617861-17.1040439188
2-0.004339321650280.1633124996830.1775900467731.172984082231.905118959123.68478176106-0.254467115487-0.05123626547690.02792124523810.0274453832534-0.1011583235330.2218696811630.5247506811950.3016590991710.1215083807970.3471345171240.0472214251392-0.01865418958450.307639237958-0.09748154267070.339524985401-11.5110118269.67382344117-13.1334429064
31.173257480211.11669575025-2.719164284716.24078122325-3.545794558988.36491094858-0.2443459155080.06921913833780.2189731617310.2145139018890.08725016718820.03009845023280.3361247548250.06270706427540.1384772733320.362017252141-0.042610243614-0.09887267181880.552139143406-0.1056723487180.7392000076721.8755847155816.612242085636.6268334406
43.8444566339-1.999823740152.495165577959.538331904662.634807335544.006892529310.1607697354940.61143545351-0.155052390442-0.2543347648730.105594583490.205363974779-0.2671771942120.708871493721-0.1834572942750.2022316197920.05266713859630.09231685132520.396409570372-0.2051444210550.31103065818216.442627178117.84705261927.4705599925
50.194945475773-0.206964120764-0.02755707659740.9939450937450.4942609693011.823510908710.1517962472280.191325967464-0.114323912291-0.0777284685306-0.019890983776-0.0887807977351-0.02019828843130.341136047197-0.09104223459410.536590982090.232109400881-0.1465020203260.606855940287-0.6405693986240.60802550131410.675121631415.113005855119.8613301669
62.708138661760.6147036721590.256834720092.72832359111-0.8551435834532.458890056360.03928564453530.655170612106-0.337088423809-0.302046377645-0.07038968939160.4503965499880.2281525563960.307974280640.03673546220480.1066917786170.079441525584-0.0172036816620.199991878313-0.1693291378840.269507446168.2649782587622.284411700825.3668990713
72.63443368752-1.09199602993-1.152885401081.771691547880.1261833071621.49994481114-0.2411105968890.3713373395010.35325492111-0.1049968692580.0009779241693180.412753820898-0.370900301509-0.5253773478650.1991836217290.269855627091-0.0226606100237-0.220966646910.8115927971710.146560447150.780486481777-22.772959944237.512754152421.0950931418
80.329124211051-1.162624553460.6867807286584.3721820918-2.069828783261.917121686850.130767124999-0.315832922313-0.541140338738-0.23525803932-0.1265393345240.605854995963-0.361786833708-0.13707711294-0.007610830703170.8296399437460.129908167552-0.0176135033350.7347134890360.4271844806171.02579706849-16.893330215252.156703457517.5124710911
95.240437049-1.762178699780.7824333527455.106358866520.5915427367123.79471463726-0.187796001430.5162529581460.813587670549-0.3424743782540.2172461088970.572498191327-0.370977254763-0.6346303201860.003382530135950.2755672062880.00127944099917-0.1273597968470.4925168201190.03355171158890.532208938815-15.464666740137.758835377921.9916265426
105.68484499155-2.009420037710.6699319579374.299655292340.6695586399063.20346974861-0.174025803404-0.1424806164620.7248893338090.1015433189630.2302857933110.783299366915-0.0771900231828-0.7480298495580.02457678368360.1672677227320.0366547220279-0.03005392459230.6475568791920.05888107989710.532107383507-20.305004238736.311403010826.8702150291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 1282 through 1395 )
2X-RAY DIFFRACTION2chain 'D' and (resid 1286 through 1395 )
3X-RAY DIFFRACTION3chain 'B' and (resid 6 through 14 )
4X-RAY DIFFRACTION4chain 'B' and (resid 15 through 32 )
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 54 )
6X-RAY DIFFRACTION6chain 'B' and (resid 55 through 125 )
7X-RAY DIFFRACTION7chain 'A' and (resid 7 through 44 )
8X-RAY DIFFRACTION8chain 'A' and (resid 45 through 54 )
9X-RAY DIFFRACTION9chain 'A' and (resid 55 through 97 )
10X-RAY DIFFRACTION10chain 'A' and (resid 98 through 126 )

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