[English] 日本語
Yorodumi
- PDB-6asb: CXXC and PHD-type zinc finger regions of FBXL19 in complex with DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6asb
TitleCXXC and PHD-type zinc finger regions of FBXL19 in complex with DNA
Components
  • DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
  • F-box/LRR-repeat protein 19
KeywordsDNA BINDING PROTEIN/DNA / CXXC zinc finger / PHD zinc finger / Structural Genomics / Structural Genomics Consortium / SGC / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


protein demethylation / unmethylated CpG binding / SCF ubiquitin ligase complex / histone demethylase activity / post-translational protein modification / transcription coregulator activity / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process ...protein demethylation / unmethylated CpG binding / SCF ubiquitin ligase complex / histone demethylase activity / post-translational protein modification / transcription coregulator activity / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of transcription by RNA polymerase II / zinc ion binding / cytosol
Similarity search - Function
PHD-finger / F-box domain / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / A Receptor for Ubiquitination Targets / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / F-box domain / Zinc/RING finger domain, C3HC4 (zinc finger) ...PHD-finger / F-box domain / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / A Receptor for Ubiquitination Targets / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / F-box domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Leucine-rich repeat domain superfamily / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / F-box/LRR-repeat protein 19
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsLiu, K. / Tempel, W. / Walker, J.R. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2018
Title: DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants.
Authors: Xu, C. / Liu, K. / Lei, M. / Yang, A. / Li, Y. / Hughes, T.R. / Min, J.
History
DepositionAug 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / citation_author
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 1.2Jan 10, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
B: DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
C: F-box/LRR-repeat protein 19
D: DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
E: DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
F: F-box/LRR-repeat protein 19
G: DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
H: DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
I: F-box/LRR-repeat protein 19
J: DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
K: DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
L: F-box/LRR-repeat protein 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,34228
Polymers84,29612
Non-polymers1,04716
Water00
1
A: DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
B: DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
C: F-box/LRR-repeat protein 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3367
Polymers21,0743
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
E: DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
F: F-box/LRR-repeat protein 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3367
Polymers21,0743
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
H: DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
I: F-box/LRR-repeat protein 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3367
Polymers21,0743
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
K: DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
L: F-box/LRR-repeat protein 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3367
Polymers21,0743
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.729, 64.282, 67.324
Angle α, β, γ (deg.)103.530, 104.660, 99.400
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.998246, 0.038379, 0.045084), (-0.03712, 0.998906, -0.028451), (-0.046127, 0.026727, 0.998578)-14.32414, 17.88999, 26.630171
3given(0.998295, -0.034811, 0.046846), (-0.035055, -0.999376, 0.004406), (0.046663, -0.006041, -0.998892)15.76452, 159.675964, -89.212349
4given(0.988613, -0.142701, -0.047748), (-0.137974, -0.986261, 0.090847), (-0.060056, -0.083224, -0.99472)8.42002, 176.291672, -57.627838
5given(1), (1), (1)
6given(0.99734, 0.018558, 0.070488), (-0.016446, 0.999402, -0.030433), (-0.071011, 0.029193, 0.997048)-11.59123, 19.090219, 24.87421
7given(0.999515, 0.02694, 0.015609), (0.027367, -0.999239, -0.027809), (0.014848, 0.028223, -0.999491)8.7529, 163.202515, -94.773323
8given(0.988396, -0.137892, -0.063713), (-0.131994, -0.987247, 0.088999), (-0.075173, -0.079557, -0.993992)7.5737, 176.664551, -59.278172
9given(1), (1), (1)
10given(0.979121, 0.174993, 0.103439), (-0.179512, 0.983095, 0.036059), (-0.09538, -0.053874, 0.993982)4.72394, 10.72021, 27.33926
11given(0.989746, -0.134362, -0.048465), (-0.136246, -0.989949, -0.037914), (-0.042883, 0.044128, -0.998105)-6.58876, 151.730301, -98.347038
12given(0.976257, -0.199452, -0.084501), (-0.203812, -0.977906, -0.046475), (-0.073365, 0.062594, -0.995339)16.35952, 166.356155, -72.735184
13given(1), (1), (1)
14given(0.958841, 0.252496, -0.129884), (-0.237521, 0.963894, 0.120379), (0.15559, -0.084575, 0.984195)-19.236099, 12.18414, 54.788712
15given(0.949345, -0.311353, -0.042472), (-0.313461, -0.947802, -0.058426), (-0.022064, 0.068779, -0.997388)24.12645, 153.941757, -68.048042
16given(0.99375, -0.111441, -0.006404), (-0.111595, -0.993172, -0.034005), (-0.002571, 0.034507, -0.999401)-4.94064, 154.016708, -95.128387

-
Components

#1: DNA chain
DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')


Mass: 3663.392 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: synthetic DNA / Source: (synth.) synthetic construct (others)
#2: Protein
F-box/LRR-repeat protein 19 / F-box and leucine-rich repeat protein 19


Mass: 13747.133 Da / Num. of mol.: 4
Fragment: CXXC and PHD-type zinc finger regions (UNP residues 31-153)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBXL19, FBL19 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q6PCT2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5 / Details: 28% PEG2000-MME, 0.1 M Bis-Tris

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.2831 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2831 Å / Relative weight: 1
ReflectionResolution: 2.85→47.91 Å / Num. obs: 19440 / % possible obs: 97.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 84.61 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.061 / Rrim(I) all: 0.117 / Net I/σ(I): 11.8 / Num. measured all: 71758 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.85-33.80.6551086428710.8430.3920.7642.197.5
9.01-47.913.60.06421686000.9810.040.07631.794.6

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
Aimless0.5.8data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: coordinates related to pdb entries 4HP3, 4O64

4hp3

4o64


Resolution: 2.85→47.91 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.862 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 3.453 / SU Rfree Blow DPI: 0.352
Details: chainsaw was used to modify the amino acid sequences of models during molecular replacement and refinement. arp/warp was used for the improvement of electron density maps. FBXL19 backbone ...Details: chainsaw was used to modify the amino acid sequences of models during molecular replacement and refinement. arp/warp was used for the improvement of electron density maps. FBXL19 backbone geometry was restrained to coordinates from PDB entry 4O64. phenix and refmac were used during intermediate refinement stages. restraints for the refinement of metal ion sites were derived from MOGUL queries of CSD structures. coot was used for interactive model building. Model geometry was assessed on the molprobity server.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 984 5.06 %thin resolution shells (sftools)
Rwork0.213 ---
obs0.215 19437 97.3 %-
Displacement parametersBiso max: 212.3 Å2 / Biso mean: 70.64 Å2 / Biso min: 22.87 Å2
Baniso -1Baniso -2Baniso -3
1-12.5687 Å27.8802 Å29.9807 Å2
2---18.4476 Å214.6191 Å2
3---5.8789 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: final / Resolution: 2.85→47.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2950 1944 16 0 4910
Biso mean--100.31 --
Num. residues----530
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1453SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes43HARMONIC2
X-RAY DIFFRACTIONt_gen_planes570HARMONIC5
X-RAY DIFFRACTIONt_it5167HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion703SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance63HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5099SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5167HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7375HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion24.43
LS refinement shellResolution: 2.85→3 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.34 162 5.65 %
Rwork0.238 2705 -
all-2867 -
obs--97.45 %
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)
15.2368-0.5743-3.3985-0.219-1.47236.0390.0502-0.16320.1145-0.3581-0.0355-0.2313-0.0704-0.0941-0.01470.19030.23360.2191-0.2305-0.0828-0.1812-74.194877.9578-33.8882
24.4098-1.2394-1.01274.13422.46547.0406-0.019-0.19310.3651-0.11550.0074-0.4950.05820.2350.01160.11730.11060.2733-0.2797-0.0069-0.1397-75.197377.1962-33.773
37.2165-1.48921.27671.8508-0.3453.4506-0.2234-0.7909-0.0437-0.0660.16320.0981-0.0063-0.53490.06020.08260.10410.1547-0.1108-0.0269-0.2202-91.045974.3665-30.0055
45.40090.9619-3.27651.52771.51222.85860.21630.6730.1482-0.4287-0.0818-0.1579-0.2097-0.0688-0.13460.33280.17330.261-0.2371-0.0904-0.3128-58.989756.0436-64.7992
56.4606-2.2953-2.7327-0.55231.22846.02080.09890.84750.18440.05960.0846-0.2938-0.4071-0.2324-0.18350.3480.12140.3195-0.294-0.0845-0.2823-60.0755.1233-64.6837
66.82011.1674-1.17382.9403-1.88867.98870.12150.25310.1061-0.62570.22170.41130.1104-0.8505-0.34320.17840.08960.0674-0.283-0.0679-0.3281-69.305749.8699-59.5449
74.04520.05741.92961.6002-1.18265.33520.05160.3425-0.2920.00010.2044-0.61340.3769-0.2604-0.2560.0925-0.24420.11050.0764-0.263-0.2534-84.246583.1709-59.6491
85.27313.60194.3371.68560.02267.1214-0.05910.3862-0.07770.13520.0068-0.1982-0.170.10390.05230.2269-0.10040.1747-0.0873-0.174-0.3182-85.203684.0706-59.7756
95.1794-0.25760.7361.47170.89972.3139-0.58060.79840.4798-0.23860.44880.1966-0.27940.14610.13180.077-0.07880.0684-0.05470.0687-0.2198-100.003987.2106-62.0443
105.17240.54410.73551.40030.92855.7360.1902-0.7761-0.12250.5293-0.0904-0.383-0.16070.2036-0.09980.2743-0.08560.0876-0.1692-0.0536-0.3173-69.5383105.4334-28.429
116.4442.09581.7918-0.4311.690413.40980.345-0.5146-0.40870.1825-0.1888-0.0207-0.31830.3915-0.15620.28560.02360.0901-0.2899-0.065-0.2834-70.7093106.3461-28.7828
121.7946-3.1205-0.94363.61960.38576.1352-0.14770.131-0.43440.51780.17830.7108-0.2021-0.7797-0.03050.13820.06080.2756-0.21760.045-0.1732-83.2626113.0498-32.4239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 12
2X-RAY DIFFRACTION2{ B|* }B1 - 12
3X-RAY DIFFRACTION3{ C|* }C35 - 152
4X-RAY DIFFRACTION4{ D|* }D1 - 12
5X-RAY DIFFRACTION5{ E|* }E1 - 12
6X-RAY DIFFRACTION6{ F|* }F35 - 148
7X-RAY DIFFRACTION7{ G|* }G1 - 12
8X-RAY DIFFRACTION8{ H|* }H1 - 12
9X-RAY DIFFRACTION9{ I|* }I33 - 153
10X-RAY DIFFRACTION10{ J|* }J1 - 12
11X-RAY DIFFRACTION11{ K|* }K1 - 12
12X-RAY DIFFRACTION12{ L|* }L33 - 150

+
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