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- PDB-6gma: Crystal structure of the FIP200 C-terminal region -

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Basic information

Entry
Database: PDB / ID: 6gma
TitleCrystal structure of the FIP200 C-terminal region
ComponentsRB1-inducible coiled-coil protein 1
KeywordsPROTEIN BINDING / autophagy / cold-shock domain / claw domain / apoptosis
Function / homology
Function and homology information


regulation of protein lipidation / ribophagy / glycophagy / Atg1/ULK1 kinase complex / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / reticulophagy / Macroautophagy / autophagosome membrane ...regulation of protein lipidation / ribophagy / glycophagy / Atg1/ULK1 kinase complex / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / reticulophagy / Macroautophagy / autophagosome membrane / positive regulation of cell size / autophagosome assembly / positive regulation of autophagy / extrinsic apoptotic signaling pathway / protein-membrane adaptor activity / liver development / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / autophagy / heart development / nuclear membrane / molecular adaptor activity / lysosome / positive regulation of protein phosphorylation / cell cycle / negative regulation of cell population proliferation / endoplasmic reticulum membrane / protein kinase binding / cytosol
Similarity search - Function
Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11
Similarity search - Domain/homology
RB1-inducible coiled-coil protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsWitt, M. / Bock, T. / Daumke, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research CouncilERC-2013-CoG-616024 Germany
CitationJournal: Mol.Cell / Year: 2019
Title: FIP200 Claw Domain Binding to p62 Promotes Autophagosome Formation at Ubiquitin Condensates.
Authors: Turco, E. / Witt, M. / Abert, C. / Bock-Bierbaum, T. / Su, M.Y. / Trapannone, R. / Sztacho, M. / Danieli, A. / Shi, X. / Zaffagnini, G. / Gamper, A. / Schuschnig, M. / Fracchiolla, D. / ...Authors: Turco, E. / Witt, M. / Abert, C. / Bock-Bierbaum, T. / Su, M.Y. / Trapannone, R. / Sztacho, M. / Danieli, A. / Shi, X. / Zaffagnini, G. / Gamper, A. / Schuschnig, M. / Fracchiolla, D. / Bernklau, D. / Romanov, J. / Hartl, M. / Hurley, J.H. / Daumke, O. / Martens, S.
History
DepositionMay 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: RB1-inducible coiled-coil protein 1
C: RB1-inducible coiled-coil protein 1
D: RB1-inducible coiled-coil protein 1
E: RB1-inducible coiled-coil protein 1
F: RB1-inducible coiled-coil protein 1


Theoretical massNumber of molelcules
Total (without water)96,4606
Polymers96,4606
Non-polymers00
Water00
1
A: RB1-inducible coiled-coil protein 1
B: RB1-inducible coiled-coil protein 1


Theoretical massNumber of molelcules
Total (without water)32,1532
Polymers32,1532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-20 kcal/mol
Surface area17160 Å2
MethodPISA
2
C: RB1-inducible coiled-coil protein 1
D: RB1-inducible coiled-coil protein 1


Theoretical massNumber of molelcules
Total (without water)32,1532
Polymers32,1532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-22 kcal/mol
Surface area17130 Å2
MethodPISA
3
E: RB1-inducible coiled-coil protein 1
F: RB1-inducible coiled-coil protein 1


Theoretical massNumber of molelcules
Total (without water)32,1532
Polymers32,1532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-19 kcal/mol
Surface area17000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.045, 187.166, 55.343
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain D and resid 1456 through 1485)
21(chain C and resid 1456 through 1485)
31(chain E and resid 1456 through 1485)
41(chain B and resid 1456 through 1485)
51(chain A and resid 1456 through 1485)
61(chain F and resid 1456 through 1485)
12(chain F and ((resid 1496 through 1503 and (name N...
22(chain A and ((resid 1496 through 1503 and (name N...
32(chain B and ((resid 1496 through 1503 and (name N...
42(chain C and ((resid 1496 through 1503 and (name N...
52(chain D and ((resid 1496 through 1503 and (name N...
62(chain E and ((resid 1496 through 1503 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAMETMET(chain D and resid 1456 through 1485)DD1456 - 14852 - 31
211ALAALAMETMET(chain C and resid 1456 through 1485)CC1456 - 14852 - 31
311ALAALAMETMET(chain E and resid 1456 through 1485)EE1456 - 14852 - 31
411ALAALAMETMET(chain B and resid 1456 through 1485)BB1456 - 14852 - 31
511ALAALAMETMET(chain A and resid 1456 through 1485)AA1456 - 14852 - 31
611ALAALAMETMET(chain F and resid 1456 through 1485)FF1456 - 14852 - 31
112ILEILEVALVAL(chain F and ((resid 1496 through 1503 and (name N...FF1496 - 150342 - 49
122ALAALALYSLYS(chain F and ((resid 1496 through 1503 and (name N...FF1456 - 15932 - 139
132ALAALALYSLYS(chain F and ((resid 1496 through 1503 and (name N...FF1456 - 15932 - 139
142ALAALALYSLYS(chain F and ((resid 1496 through 1503 and (name N...FF1456 - 15932 - 139
152ALAALALYSLYS(chain F and ((resid 1496 through 1503 and (name N...FF1456 - 15932 - 139
212ILEILEVALVAL(chain A and ((resid 1496 through 1503 and (name N...AA1496 - 150342 - 49
222GLYGLYLYSLYS(chain A and ((resid 1496 through 1503 and (name N...AA1455 - 15931 - 139
232GLYGLYLYSLYS(chain A and ((resid 1496 through 1503 and (name N...AA1455 - 15931 - 139
242GLYGLYLYSLYS(chain A and ((resid 1496 through 1503 and (name N...AA1455 - 15931 - 139
252GLYGLYLYSLYS(chain A and ((resid 1496 through 1503 and (name N...AA1455 - 15931 - 139
312ILEILEVALVAL(chain B and ((resid 1496 through 1503 and (name N...BB1496 - 150342 - 49
322GLYGLYLYSLYS(chain B and ((resid 1496 through 1503 and (name N...BB1455 - 15931 - 139
332GLYGLYLYSLYS(chain B and ((resid 1496 through 1503 and (name N...BB1455 - 15931 - 139
342GLYGLYLYSLYS(chain B and ((resid 1496 through 1503 and (name N...BB1455 - 15931 - 139
352GLYGLYLYSLYS(chain B and ((resid 1496 through 1503 and (name N...BB1455 - 15931 - 139
412ILEILEVALVAL(chain C and ((resid 1496 through 1503 and (name N...CC1496 - 150342 - 49
422GLYGLYLYSLYS(chain C and ((resid 1496 through 1503 and (name N...CC1455 - 15931 - 139
432GLYGLYLYSLYS(chain C and ((resid 1496 through 1503 and (name N...CC1455 - 15931 - 139
442GLYGLYLYSLYS(chain C and ((resid 1496 through 1503 and (name N...CC1455 - 15931 - 139
452GLYGLYLYSLYS(chain C and ((resid 1496 through 1503 and (name N...CC1455 - 15931 - 139
512ILEILEVALVAL(chain D and ((resid 1496 through 1503 and (name N...DD1496 - 150342 - 49
522GLYGLYLYSLYS(chain D and ((resid 1496 through 1503 and (name N...DD1455 - 15931 - 139
532GLYGLYLYSLYS(chain D and ((resid 1496 through 1503 and (name N...DD1455 - 15931 - 139
542GLYGLYLYSLYS(chain D and ((resid 1496 through 1503 and (name N...DD1455 - 15931 - 139
552GLYGLYLYSLYS(chain D and ((resid 1496 through 1503 and (name N...DD1455 - 15931 - 139
612ILEILEVALVAL(chain E and ((resid 1496 through 1503 and (name N...EE1496 - 150342 - 49
622GLYGLYASNASN(chain E and ((resid 1496 through 1503 and (name N...EE1455 - 15911 - 137
632GLYGLYASNASN(chain E and ((resid 1496 through 1503 and (name N...EE1455 - 15911 - 137
642GLYGLYASNASN(chain E and ((resid 1496 through 1503 and (name N...EE1455 - 15911 - 137
652GLYGLYASNASN(chain E and ((resid 1496 through 1503 and (name N...EE1455 - 15911 - 137

NCS ensembles :
ID
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: 16076.677 Da / Num. of mol.: 6
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

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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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.0, 1.0 M LiCl, 14% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.17→37.758 Å / Num. obs: 16476 / % possible obs: 97.1 % / Redundancy: 3.657 % / Biso Wilson estimate: 135.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.081 / Χ2: 1.053 / Net I/σ(I): 11.02
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.17-3.363.7781.9890.5626240.2392.30398.4
3.36-3.593.6160.8141.4824710.6250.9598.1
3.59-3.883.7080.3743.2722990.9090.43497.9
3.88-4.243.8870.1617.6621620.9840.18698.3
4.24-4.743.7330.08813.4819230.9950.10197.9
4.74-5.463.3920.06516.7717060.9970.07795.8
5.46-6.673.7250.05521.414600.9970.06396.2
6.67-9.343.440.03134.0411590.9990.03695.2
9.34-37.7583.1090.02340.396720.9990.02789.6

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→37.758 Å / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.09
RfactorNum. reflection% reflection
Rfree0.2948 1594 9.98 %
Rwork0.2665 --
obs0.2693 15973 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 271.65 Å2 / Biso mean: 153.9785 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.2→37.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5952 0 0 0 5952
Num. residues----758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046054
X-RAY DIFFRACTIONf_angle_d0.828156
X-RAY DIFFRACTIONf_chiral_restr0.049931
X-RAY DIFFRACTIONf_plane_restr0.0041027
X-RAY DIFFRACTIONf_dihedral_angle_d17.1743729
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11D935X-RAY DIFFRACTION16.825TORSIONAL
12C935X-RAY DIFFRACTION16.825TORSIONAL
13E935X-RAY DIFFRACTION16.825TORSIONAL
14B935X-RAY DIFFRACTION16.825TORSIONAL
15A935X-RAY DIFFRACTION16.825TORSIONAL
16F935X-RAY DIFFRACTION16.825TORSIONAL
21F1805X-RAY DIFFRACTION16.825TORSIONAL
22A1805X-RAY DIFFRACTION16.825TORSIONAL
23B1805X-RAY DIFFRACTION16.825TORSIONAL
24C1805X-RAY DIFFRACTION16.825TORSIONAL
25D1805X-RAY DIFFRACTION16.825TORSIONAL
26E1805X-RAY DIFFRACTION16.825TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2002-3.30340.39061320.41191297142998
3.3034-3.42140.42861510.38961307145898
3.4214-3.55830.36521390.37171282142198
3.5583-3.72010.36971440.32871303144798
3.7201-3.91610.38031450.31871291143698
3.9161-4.16110.32851470.30681310145798
4.1611-4.4820.28741430.26841311145498
4.482-4.93210.29511450.24721311145698
4.9321-5.64380.2821460.26691300144696
5.6438-7.10280.34191510.2881318146996
7.1028-37.76020.22651510.20761349150093
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)
12.25440.96131.31562.36382.27241.6486-0.1109-0.47291.442-0.22750.02030.28421.0509-0.09510.42311.2568-0.0020.12171.85250.45070.947919.4606-11.871737.6353
27.4304-0.45153.29648.8485-0.472710.8864-0.16360.3721-0.6572-0.14850.3147-1.22790.89321.0039-0.12810.71790.18530.05240.9934-0.06360.818-31.2691-14.32818.6549
38.7263-2.9184-0.40899.9115-0.0465.60261.37241.77260.0672-0.7285-1.15240.5181-0.00580.2264-0.58111.28250.0731-0.00881.53470.40540.994119.7549-8.734828.6838
49.10980.4226-0.96257.3201-2.09969.82710.2587-1.6569-0.52362.1659-0.0101-1.40811.484-0.18940.22972.16090.1603-0.53851.45360.16141.1962-30.4439-26.948131.5087
57.4088-2.0262-2.03423.24582.77722.27720.9829-0.23380.4233-0.1511-0.0291-0.0109-1.1107-0.5275-0.81051.52460.13910.24451.27170.1560.609740.5911-14.874418.8493
611.1167-0.0811.8299.68121.91829.82060.5260.44840.0813-1.425-0.25651.4507-1.201-1.0206-0.23921.19560.1087-0.14351.03520.15371.122866.2315-58.7698-5.2094
73.81590.37463.924310.0974-2.54526.6094-0.1974-1.0567-2.06830.2571.38951.16220.4292-0.9876-1.19411.3043-0.10740.13131.17170.27150.819437.4334-19.597811.2326
88.9590.5339-0.217410.0478-3.6584.34060.218-0.73040.87661.6298-0.73960.2939-1.71230.25570.42211.6523-0.08710.03691.2081-0.26911.008479.1603-44.970113.2355
91.9802-0.15893.43955.32310.17172.66340.10980.8340.1675-1.93050.1485-0.5903-0.1564-0.2535-0.22951.6204-0.1230.29661.29010.13310.69434.1478-22.2911-6.1741
105.39840.03671.35355.6044-0.61220.88880.5711-0.53381.22430.67760.08430.8767-0.5419-0.2329-0.68041.86210.12940.59632.3224-0.01271.979554.5574-64.578223.0645
115.54520.26351.25132.68840.85968.2334-0.723-0.27740.09771.07721.2571-0.33280.66660.9321-0.68391.0543-0.11960.02590.9907-0.01130.689938.758-20.24862.0473
127.12983.80390.64423.39891.26161.2219-0.26990.52580.1345-0.71690.58392.1941-0.1161-1.7864-0.12411.31740.1542-0.31172.17420.29382.287540.6305-78.88175.6099
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and resid 1456 through 1486A1456 - 1486
2X-RAY DIFFRACTION2chain 'A' and resid 1495 through 1593A1495 - 1593
3X-RAY DIFFRACTION3chain 'B' and resid 1455 through 1486B1455 - 1486
4X-RAY DIFFRACTION4chain 'B' and resid 1495 through 1593B1495 - 1593
5X-RAY DIFFRACTION5chain 'C' and resid 1455 through 1486C1455 - 1486
6X-RAY DIFFRACTION6chain 'C' and resid 1495 through 1593C1495 - 1593
7X-RAY DIFFRACTION7chain 'D' and resid 1455 through 1486D1455 - 1486
8X-RAY DIFFRACTION8chain 'D' and resid 1495 through 1593D1495 - 1593
9X-RAY DIFFRACTION9chain 'E' and resid 1455 through 1486E1455 - 1486
10X-RAY DIFFRACTION10chain 'E' and resid 1495 through 1591E1495 - 1591
11X-RAY DIFFRACTION11chain 'F' and resid 1456 through 1485F1456 - 1485
12X-RAY DIFFRACTION12chain 'F' and resid 1495 through 1593F1495 - 1593

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