[English] 日本語
Yorodumi
- PDB-7ea2: crystal structure of NAP1 FIR in complex with RB1CC1 Claw domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ea2
Titlecrystal structure of NAP1 FIR in complex with RB1CC1 Claw domain
Components5-azacytidine-induced protein 2,RB1-inducible coiled-coil protein 1
KeywordsPROTEIN BINDING / FIR / complex
Function / homology
Function and homology information


regulation of protein lipidation / ribophagy / glycophagy / Atg1/ULK1 kinase complex / dendritic cell differentiation / serine/threonine protein kinase complex / dendritic cell proliferation / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site ...regulation of protein lipidation / ribophagy / glycophagy / Atg1/ULK1 kinase complex / dendritic cell differentiation / serine/threonine protein kinase complex / dendritic cell proliferation / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / reticulophagy / Macroautophagy / type I interferon-mediated signaling pathway / autophagosome membrane / positive regulation of cell size / autophagosome assembly / canonical NF-kappaB signal transduction / positive regulation of autophagy / extrinsic apoptotic signaling pathway / negative regulation of canonical NF-kappaB signal transduction / protein-membrane adaptor activity / T cell activation / liver development / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / autophagy / heart development / mitotic cell cycle / nuclear membrane / defense response to virus / molecular adaptor activity / lysosome / positive regulation of protein phosphorylation / cell cycle / negative regulation of cell population proliferation / endoplasmic reticulum membrane / protein kinase binding / cytoplasm / cytosol
Similarity search - Function
Tbk1/Ikki binding domain / TBD domain / Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11
Similarity search - Domain/homology
CITRATE ANION / DI(HYDROXYETHYL)ETHER / RB1-inducible coiled-coil protein 1 / 5-azacytidine-induced protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: 5-azacytidine-induced protein 2,RB1-inducible coiled-coil protein 1
A: 5-azacytidine-induced protein 2,RB1-inducible coiled-coil protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5626
Polymers27,8782
Non-polymers6844
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-10 kcal/mol
Surface area12120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.620, 67.620, 247.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11B-1719-

HOH

21A-1813-

HOH

-
Components

#1: Protein 5-azacytidine-induced protein 2,RB1-inducible coiled-coil protein 1 / FAK family kinase-interacting protein of 200 kDa / FIP200


Mass: 13938.976 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 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9H6S1, UniProt: Q8TDY2
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M phosphate/citrate pH 4.2, 40% PEG300

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.14→247.37 Å / Num. obs: 19420 / % possible obs: 99.7 % / Redundancy: 37.4 % / Biso Wilson estimate: 43.4 Å2 / CC1/2: 0.997 / Net I/σ(I): 16
Reflection shellResolution: 2.14→2.2 Å / Num. unique obs: 1384 / CC1/2: 0.844

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CZG

7czg


Resolution: 2.14→58.56 Å / SU ML: 0.2119 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8331
RfactorNum. reflection% reflection
Rfree0.2323 1023 5.28 %
Rwork0.2009 18337 -
obs0.2026 19360 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.77 Å2
Refinement stepCycle: LAST / Resolution: 2.14→58.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1777 0 46 66 1889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751878
X-RAY DIFFRACTIONf_angle_d0.89072524
X-RAY DIFFRACTIONf_chiral_restr0.0571274
X-RAY DIFFRACTIONf_plane_restr0.0059314
X-RAY DIFFRACTIONf_dihedral_angle_d11.32691587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.250.26291420.2422548X-RAY DIFFRACTION98.72
2.25-2.390.30671330.22392516X-RAY DIFFRACTION99.03
2.39-2.580.27381590.22412541X-RAY DIFFRACTION99.12
2.58-2.840.26431480.2272580X-RAY DIFFRACTION99.49
2.84-3.250.2261180.20962643X-RAY DIFFRACTION99.6
3.25-4.090.19811360.18712659X-RAY DIFFRACTION99.75
4.09-58.560.22931870.18942850X-RAY DIFFRACTION99.61
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)
11.85528143139-0.04875276326890.07218560491097.1935171425-2.931681467823.743390645850.1719846817170.6328669127380.107639122138-0.778869064739-0.0710914569338-0.7135663065010.04877795610211.00496800055-0.03987818437880.6166334695380.01421460299470.170464390920.6517707131210.0863797254180.424855068769-38.681-14.35112.707
23.23640460184-3.20388800991-1.276946681345.23145466392.167396137842.83949725234-0.190612020582-0.168261977491-0.08462314635070.377502144817-0.151897565640.3539067949840.334403214770.175759685929-0.1781786353130.4427421874660.0190596044171-0.000824404249270.41376229222-0.005962883236580.41156976127-27.33-29.225.993
32.883479196510.111064516787-0.5356168682132.815271798890.5153238580832.13318180193-0.02751413603910.1122306677980.117386027092-0.426535307781-0.02539321345060.180983093685-0.2948565050410.1450083599250.1169385466360.436646256121-0.0304372180909-0.01462672543440.2350658017320.008119220762580.260538474579-11.659-19.587-8.348
43.621564291820.828808466531-0.08464835079112.048079599920.6379422369493.39912962709-0.0169756024-0.1125315993660.278596034003-0.0808193829682-0.1907281424250.116303252039-0.427225021170.007108560948860.1463603402040.4835959273560.0266039209046-0.04617904116020.1899038467910.009914966705880.332433535249-8.664-17.203-13.135
53.542381132461.37182127724-1.59732171371.72482616338-1.031174789316.89484437501-0.356541579683-0.7783697403931.44195564966-0.08857405085570.0622016277854-1.01924637771-1.182321828821.03913235227-0.02700987489760.601927950144-0.08390731039290.008172514659660.374797016528-0.05793464790080.506502228579-18.548-17.598-21.595
67.33642477866-0.2235116476930.4459977437013.608191879991.01006801842.761582101090.0848256016229-0.278811930934-0.1353884092940.340175489676-0.04228658078290.2562407378690.08128001147320.0577012243857-0.004261467272930.346748502349-0.009622830837650.04908883833860.223702523928-0.03914305021230.384098472804-8.811-24.005-13.581
72.73133321110.3065721631081.01548970582.16629535240.9355098247742.16093765922-0.0522170765157-0.2485010396471.873085054580.135383379909-0.01915096164141.37110451803-1.58094071997-0.4423849637980.04097236123190.6358782453310.137639742926-0.006416211675150.365884421503-0.03358877000730.8480929362053.461-11.63-18.073
86.231350815280.9829778771633.177655940365.40979307181-0.4438054698725.74580656558-0.452016139219-0.12963880368-0.07824754700670.02125457028890.168405720429-0.556361311501-0.4151272532890.3460314869580.1056994104070.3601019309160.009923124279160.01227160373220.286322978713-0.01296338317990.363661820172-9.606-24.418-14.663
93.03475174534-1.772647422410.1374806581252.04133046404-1.298081678131.689540958130.105199342447-0.6635745096880.5816659588170.4920532240270.3290841847890.180784239609-0.254354818856-0.524633130555-0.1306095081750.5909913367870.02124688488130.1114745653810.344945547114-0.06970053180950.5126741640033.091-23.244-19.028
101.654369843030.985146350569-1.840338807840.942565408346-1.249272118532.64171842633-0.1710179306770.345781875872-0.316360910081-0.579485339436-0.118377175914-0.4359059371540.265213725553-0.3416356508860.01006480306190.603858017613-0.00011849560889-0.03970289959540.290181004590.04888319721920.427300350874-7.764-32.286-4.809
111.79199289711-1.74371837578-1.175075674814.284311278380.6443282926022.489411467450.136988153909-0.04048977275650.1907906837950.00233488808039-0.11155133524-0.0706043333209-0.391144415316-0.02776600865310.03998029542160.4518802716650.02811454274370.004029727940410.277695205318-0.00826398298920.321022228584-22.452-19.6412.945
123.247516712960.956620374181-0.03566337628462.50958425720.9831525733624.203644016650.2291895149940.2208936811570.747108280838-0.565883995159-0.1766655059210.0425327354218-0.879791489863-0.260843476121-0.06723213030030.7211582882580.09663087820730.07317112425090.3267220996640.06811496199360.41660763286-24.594-9.9756.922
135.35022447091-0.9195785081060.3741086944743.314657479451.046595000153.392138357660.5454570225620.6168273554520.185388134092-0.0749514962841-0.410638951584-0.255224003722-0.7055585438250.0360673251225-0.03991092064770.4980670565170.05971499861860.04452677201390.3276912575030.08807974343840.322881186333-26.544-17.6989.104
143.8091496149-1.087589419421.046995940154.020865896791.72016522853.163386524180.0369651434070.04624846943520.806814856036-0.330644334373-0.151257736484-0.431904665144-0.8199108007970.00928552656016-0.06656212505720.6265785979760.04719259714240.07925844218330.3476265519140.1166731513380.42729400161-32.556-10.6877.678
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1475 through 1484 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1485 through 1494 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1495 through 1515 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1516 through 1534 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1535 through 1553 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1554 through 1566 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1567 through 1580 )
8X-RAY DIFFRACTION8chain 'A' and (resid 1581 through 1591 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1475 through 1484 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1485 through 1494 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1495 through 1512 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1513 through 1553 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1554 through 1566 )
14X-RAY DIFFRACTION14chain 'B' and (resid 1567 through 1591 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more