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- PDB-9j54: Crystal structure of FIP200 Claw in complex with ATG16L1 -

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Basic information

Entry
Database: PDB / ID: 9j54
TitleCrystal structure of FIP200 Claw in complex with ATG16L1
Components
  • Autophagy-related protein 16-1
  • RB1-inducible coiled-coil protein 1
KeywordsPROTEIN BINDING / FIP200 / ATG16L1
Function / homology
Function and homology information


C-terminal protein lipidation / Atg12-Atg5-Atg16 complex / negative regulation of dendrite extension / vacuole-isolation membrane contact site / ubiquitin-like protein transferase activity / microautophagy / Atg1/ULK1 kinase complex / ribophagy / glycophagy / dendrite arborization ...C-terminal protein lipidation / Atg12-Atg5-Atg16 complex / negative regulation of dendrite extension / vacuole-isolation membrane contact site / ubiquitin-like protein transferase activity / microautophagy / Atg1/ULK1 kinase complex / ribophagy / glycophagy / dendrite arborization / xenophagy / corpus callosum development / protein localization to phagophore assembly site / phagophore assembly site membrane / autophagy of mitochondrion / pexophagy / piecemeal microautophagy of the nucleus / negative stranded viral RNA replication / endolysosome membrane / phagophore assembly site / reticulophagy / axonal transport / Macroautophagy / autophagosome membrane / axoneme / autophagosome assembly / positive regulation of cell size / extrinsic apoptotic signaling pathway / protein-membrane adaptor activity / sperm midpiece / positive regulation of autophagy / autophagosome / negative regulation of extrinsic apoptotic signaling pathway / hippocampus development / positive regulation of JNK cascade / macroautophagy / liver development / autophagy / protein transport / heart development / GTPase binding / nuclear membrane / molecular adaptor activity / defense response to virus / lysosome / axon / negative regulation of cell population proliferation / innate immune response / endoplasmic reticulum membrane / protein kinase binding / glutamatergic synapse / identical protein binding / cytosol
Similarity search - Function
Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11 / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. ...Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11 / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Autophagy-related protein 16-1 / RB1-inducible coiled-coil protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsGong, X.Y. / Pan, L.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21822705 China
CitationJournal: To be published
Title: Mechanistic insights into the FIP200-interacting region of ATG16L1
Authors: Gong, X.Y.
History
DepositionAug 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RB1-inducible coiled-coil protein 1
B: Autophagy-related protein 16-1
C: RB1-inducible coiled-coil protein 1
D: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)28,8654
Polymers28,8654
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-15 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.701, 34.894, 60.727
Angle α, β, γ (deg.)90.000, 118.377, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 12614.555 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 (E. coli) / References: UniProt: Q8TDY2
#2: Protein/peptide Autophagy-related protein 16-1 / APG16-like 1


Mass: 1817.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG16L1, APG16L, UNQ9393/PRO34307 / Production host: Escherichia coli (E. coli) / References: UniProt: Q676U5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.9 Å3/Da / Density % sol: 35.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% v/v 2-Propanol, 0.1 M BICINE (pH 8.5), 30% w/v Polyethylene glycol 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.61→53.43 Å / Num. obs: 27862 / % possible obs: 98 % / Redundancy: 6.2 % / Biso Wilson estimate: 25.26 Å2 / Rpim(I) all: 0.021 / Net I/σ(I): 17.2
Reflection shellResolution: 1.61→1.64 Å / Num. unique obs: 1383 / Rpim(I) all: 0.29

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Processing

Software
NameVersionClassification
PHENIX1.19rc4_4035refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→22.46 Å / SU ML: 0.1773 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9877
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2157 1303 4.69 %
Rwork0.178 26498 -
obs0.1797 27801 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.91 Å2
Refinement stepCycle: LAST / Resolution: 1.61→22.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 0 139 1823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01391755
X-RAY DIFFRACTIONf_angle_d1.26562379
X-RAY DIFFRACTIONf_chiral_restr0.0746269
X-RAY DIFFRACTIONf_plane_restr0.0117297
X-RAY DIFFRACTIONf_dihedral_angle_d15.4301644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.670.28891290.25652975X-RAY DIFFRACTION98.63
1.67-1.750.23311270.21752994X-RAY DIFFRACTION99.49
1.75-1.840.22081390.19472969X-RAY DIFFRACTION99.42
1.84-1.960.20971320.19372974X-RAY DIFFRACTION99.71
1.96-2.110.24221020.17572562X-RAY DIFFRACTION85.14
2.11-2.320.21751680.17042971X-RAY DIFFRACTION99.87
2.32-2.660.20921810.18282979X-RAY DIFFRACTION99.81
2.66-3.350.22281900.18192975X-RAY DIFFRACTION99.62
3.35-22.460.20381350.16613099X-RAY DIFFRACTION99.11

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