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- PDB-7czg: Crystal structure of FIP200 Claw domain apo form -

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Open data


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Basic information

Entry
Database: PDB / ID: 7czg
TitleCrystal structure of FIP200 Claw domain apo form
ComponentsRB1-inducible coiled-coil protein 1
KeywordsSIGNALING PROTEIN / autophagy / FIP200
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
DI(HYDROXYETHYL)ETHER / RB1-inducible coiled-coil protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhou, Z.X. / Pan, L.F.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31470749 China
National Natural Science Foundation of China (NSFC)21621002 China
CitationJournal: Nat Commun / Year: 2021
Title: Phosphorylation regulates the binding of autophagy receptors to FIP200 Claw domain for selective autophagy initiation.
Authors: Zhou, Z. / Liu, J. / Fu, T. / Wu, P. / Peng, C. / Gong, X. / Wang, Y. / Zhang, M. / Li, Y. / Wang, Y. / Xu, X. / Li, M. / Pan, L.
History
DepositionSep 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8687
Polymers49,5494
Non-polymers3183
Water3,765209
1
A: RB1-inducible coiled-coil protein 1
C: RB1-inducible coiled-coil protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8813
Polymers24,7752
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-9 kcal/mol
Surface area11630 Å2
MethodPISA
2
B: RB1-inducible coiled-coil protein 1
D: RB1-inducible coiled-coil protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9874
Polymers24,7752
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-8 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.544, 75.616, 99.364
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,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: 12387.336 Da / Num. of mol.: 4
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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: Sodium citrate tribasic dihydrate pH 5.0, Jeffamine ED-2001 pH 7.0

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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: DECTRIS PILATUS3 S 6M / Detector: PIXEL / 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: 1.8→60.17 Å / Num. obs: 41526 / % possible obs: 90.6 % / Redundancy: 12.9 % / Biso Wilson estimate: 27.14 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.7
Reflection shellResolution: 1.8→1.9 Å / Num. unique obs: 5232 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DCE

6dce


Resolution: 1.8→39.37 Å / SU ML: 0.1986 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.0055
RfactorNum. reflection% reflection
Rfree0.2295 1995 4.83 %
Rwork0.1892 39350 -
obs0.1912 41345 90.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.21 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 21 209 3418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583283
X-RAY DIFFRACTIONf_angle_d0.79714420
X-RAY DIFFRACTIONf_chiral_restr0.0551482
X-RAY DIFFRACTIONf_plane_restr0.0056549
X-RAY DIFFRACTIONf_dihedral_angle_d13.33691980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.35421750.30663043X-RAY DIFFRACTION99.84
1.85-1.90.3219910.29321760X-RAY DIFFRACTION99.2
1.9-1.950.30021630.25123059X-RAY DIFFRACTION99.48
1.95-2.010.22841630.21263019X-RAY DIFFRACTION99.78
2.01-2.090.28081090.21542156X-RAY DIFFRACTION70.12
2.09-2.170.28831360.1963088X-RAY DIFFRACTION99.94
2.17-2.270.24661190.1982455X-RAY DIFFRACTION79.32
2.27-2.390.25531390.2063104X-RAY DIFFRACTION99.75
2.39-2.540.25531660.20343067X-RAY DIFFRACTION99.85
2.54-2.730.2773920.22821864X-RAY DIFFRACTION60.24
2.73-3.010.21531530.20213145X-RAY DIFFRACTION100
3.01-3.440.24691570.18713135X-RAY DIFFRACTION100
3.44-4.340.19291650.15333169X-RAY DIFFRACTION99.97
4.34-39.370.19271670.17053286X-RAY DIFFRACTION99.2
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)
14.41043391006-1.60588634814-0.3873712525873.963907869040.5079456183973.093675338390.0384254587741-0.648065752836-0.05927159521160.251086940757-0.1793248180380.2430994698880.524050927165-0.4200978020050.1451528121490.330942691254-0.0558797201957-0.01867958010950.4157338749030.00484072197130.2374805410072.6816095402-9.58257025916-34.3912508299
25.4987094841.09154194624-1.371234652812.47666020758-0.6375497570316.84372857098-0.05187742140510.3724155319580.223706520794-0.1904980199990.1897596073560.190827986979-0.199481191298-0.1766420759730.007153915432750.249636905212-0.00188213859915-0.04444605382320.244596615080.03203226907430.2215607765878.7259998434-7.87335405612-49.1737798865
33.028173337030.8040832587620.722706547192.491255047090.4344291957422.050459464740.08606488488940.135292476936-0.165084414022-0.1596307307350.0202772481588-0.1638998882620.279579365033-0.0840031853016-0.09334544898470.26145600573-0.0144353053738-0.02707410429030.23355169725-0.003691099643030.23480961065210.4050827293-11.4054340274-44.6462790902
41.81363451722-1.340176368560.6859274447266.83534203663-1.607641393956.679226474370.04749536340120.407512009114-0.391763933511-0.399741060823-0.105808159758-0.7401634826030.9157624931870.4389022133360.0850729667470.3256904130090.0603146347965-0.04082874654720.458976847465-0.06881007606050.4044613009164.9529002252-14.3689248625-56.5475529095
54.86732544777-0.2626938280221.38426704541.22971837872-0.201547364292.069678622750.296944368534-0.416806563302-0.5035823992990.132133659255-0.0889111404376-0.09903612892950.228914203406-0.10217065359-0.1842915969890.278185748511-0.024847427187-0.03658366729320.262481175138-0.0006424674855690.26573549476510.3370817839-14.0033139307-40.7286550306
68.12098246866-0.9218255002551.672647911716.190347033921.172710858048.95545253932-0.3036190928571.36100611033-0.179004821209-0.689322399486-0.21169233224-0.702286752040.3865112548141.032764527830.4149901332190.341493687792-0.0001765346925040.06243880921890.5165767903180.03942153668420.38329499352124.4312999346-7.55955908958-48.9142279665
72.981355971220.628236074004-0.1746998790115.031888731740.01927080880694.038794409220.103158705851-0.264123862342-0.55245566057-0.0527415930023-0.2040195371920.05642344705570.598081438661-0.393151332859-0.01162873317260.280183772124-0.0318113347437-0.03663621737720.257846458652-0.002404056833790.2359253925889.4826878223-14.7814126741-41.5267531233
84.257446547080.146078286991-0.2339369587131.15574579297-0.4513240004233.423562419-0.127789134649-0.05918754235470.133939865131-0.02564024248120.1195176748370.01111844215920.03312604721360.0982385534624-0.0006692079820220.226403380185-0.0055671417121-0.01266145696670.163029615085-0.005134440931580.205778572282-3.93282437082-6.53815117362-74.5354282731
94.385407222910.0775791762927-1.149633389012.691424035241.106837165074.51733236084-0.23003380122-0.341705407379-0.1408277910160.3306581646810.1133428136260.1134580822570.416629590252-0.1888716666090.1384095081370.2797434921020.02294167834390.03105738133140.2311627408550.01244655141160.227000970236-8.97381610761-9.63023554194-69.7181011706
102.2582990960.4560745278641.709287486996.601918670741.75646311341.614529030670.0380350619349-1.12142234621-0.6040436562220.692389891826-0.2886096128620.4823134897051.53333050560.1495653325480.2328177261290.5748594692710.003802436450630.054182585870.5324595956870.1020638718540.391596230303-4.53809319962-15.7309824587-57.2853096587
112.577226079610.6064246673950.611975356742.521919085051.667630727652.1295162974-0.324989820727-0.184257689584-0.3918887157410.206144106759-0.1151260475350.4876633468640.222850035703-0.6940632666690.3431832431190.299030099584-0.000710284972890.06412810791270.41519287710.03593620117890.246278521505-15.9272614487-9.55292859372-70.3490882841
125.42180408526-1.7129159558-0.9994495559433.759674736881.228896444453.35257725624-0.4817430014090.29175587638-0.1618479167440.2940306309860.206583779759-0.2877530100710.447952040324-0.1390048682280.279453493740.338184722149-0.03437608026820.03036561465120.1764469928550.009679448350370.262768319849-6.71152766161-13.4663181919-74.607737282
133.126800969770.1909779409721.247128034840.808070913293-0.5688903998082.746442620090.241028361523-0.237423110113-0.4053797251030.0772513308475-0.0156180914679-0.01733885613640.2323999802910.145935947-0.1752272187570.282554506435-0.0219183152576-0.004496672209710.363167855386-0.04417331038160.335643356672-4.81258106697-3.24421530553-34.0361001824
143.037011417021.011763843930.4545212962892.87158663475-0.5402773175092.3890113163-0.08065608151660.53131022398-0.0968043837243-0.3068578906010.166446548209-0.0443137014853-0.0276936391985-0.169218503338-0.05154194285570.279581116565-0.01714027380980.01283889538230.451059430544-0.06530758230990.277340199861-13.68207835390.597470491294-47.0440261176
154.222916247-0.501754915953-4.679366713366.99225187112.987688385556.991584050510.2256216556140.5730655993321.15058738283-1.22781796815-0.28891843648-0.514814529607-1.46782780181.088024428840.02588902917070.584489276841-0.03998663607620.04989379394250.628355810060.04694801347930.508432480895-5.8605159752210.977505185-48.4436269681
164.06621821926-0.00701603917477-0.4711354739841.60756537241-0.05313579681111.995151861150.19309941346-0.0732269701360.321806925488-0.0461167279069-0.0912546086446-0.0948400920924-0.06167917715410.0824153782547-0.04507100638370.288249295846-0.005818197986820.02688094133880.322498557783-0.02946571479920.243161129086-13.64842459513.01277572984-39.1895987076
174.454962737221.1342344922-1.224260277612.799780643010.07497357961663.32582641875-0.1819418568851.950349568410.363568273511-0.3208858666760.2822054804340.227423714923-0.721639933023-0.8342913597390.01992811929480.3547600479760.00600001857289-0.0246785776750.7239111459110.03424601688740.287935245865-25.95664242781.29935155231-51.8327465338
182.752598348570.6112959101981.024749790962.727394891970.9315021290952.860781487920.0176888028360.178673191738-0.0155490910557-0.08833944926760.0339544406777-0.329621020268-0.1501948403110.321344972917-0.0717410130340.272908724445-0.02712558401990.02246025328950.395701104163-0.03215431300990.328433700202-11.11976352024.10666278405-39.0163866763
193.205514496310.480577710752.353524551210.02148751540030.3248099523892.789426844610.03513608150490.389323245024-0.262154976198-0.1427777322930.0816484625922-0.05765072936870.0131680207249-0.144586398963-0.1132212377930.2989580015990.01066696286370.03313650882180.3337051749810.01088608453440.2708773762124.84197435752-2.6728227263-84.9576674308
202.57903504728-0.233401273031-0.6471933902841.70912424469-0.1919844100241.04084161763-0.0405137787575-0.355744188434-0.1457622510320.3239412558560.0390213063378-0.0635587026843-0.004340363287070.1891558376470.01730983279670.262803278650.010539813085-0.00666480459440.2833611931790.03679546683710.2470527439213.99949082610.948611204316-68.1284341663
213.075536795092.99338049173-3.654250884084.63542669476-2.828741352765.390880476030.559913126518-0.2330579057530.4986937465211.56722993913-0.09369253160390.780100380907-0.607614790899-0.0506930222398-0.4914797614270.614116400911-0.03874850315720.1517899197740.353139399543-0.06248941260770.3960396112548.4147827604410.988610125-64.7174021078
222.87569997053-0.338987435412-0.7389291807221.76593873443-0.1043513270252.40538594076-0.0163299177717-0.08327419132620.2024169697730.09562259374580.1641902499660.00103677255439-0.11111361250.221528426067-0.207325456220.2710292364760.009993883894320.03464974380670.1830335481120.0008804907481920.24136823799315.37714969954.31656788117-75.2879642616
233.45210018765-1.231158762010.01451427260033.00043369376-0.5580661299334.35976049556-0.116289302776-0.5058638407370.1405596528660.3061490818240.193365510242-0.121666979664-0.201605717130.53168863996-0.1213470587120.225924104078-0.0120978054590.01118580630950.310737538904-0.02926549015510.24557727602221.26790615423.16486965313-68.674782405
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1493 through 1505 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1506 through 1520 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1521 through 1538 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1539 through 1553 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1554 through 1566 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1567 through 1580 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1581 through 1591 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1493 through 1515 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1516 through 1538 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1539 through 1553 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1554 through 1580 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1581 through 1592 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1487 through 1512 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1513 through 1534 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1535 through 1553 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1554 through 1566 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1567 through 1580 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1581 through 1592 )
19X-RAY DIFFRACTION19chain 'D' and (resid 1487 through 1505 )
20X-RAY DIFFRACTION20chain 'D' and (resid 1506 through 1534 )
21X-RAY DIFFRACTION21chain 'D' and (resid 1535 through 1553 )
22X-RAY DIFFRACTION22chain 'D' and (resid 1554 through 1566 )
23X-RAY DIFFRACTION23chain 'D' and (resid 1567 through 1592 )

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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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