[English] 日本語
Yorodumi
- PDB-6imq: Crystal structure of PML B1-box multimers -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6imq
TitleCrystal structure of PML B1-box multimers
ComponentsProtein PML
KeywordsONCOPROTEIN / TRIM19 / PML / nuclear body / B1-box / PML-RARA / APL / leukemia
Function / homology
Function and homology information


regulation of calcium ion transport into cytosol / ubiquitin-like protein ligase activity / negative regulation of translation in response to oxidative stress / positive regulation of protein localization to chromosome, telomeric region / suppression of viral release by host / PML body organization / SUMO binding / positive regulation of apoptotic process involved in mammary gland involution / fibroblast migration / SMAD protein signal transduction ...regulation of calcium ion transport into cytosol / ubiquitin-like protein ligase activity / negative regulation of translation in response to oxidative stress / positive regulation of protein localization to chromosome, telomeric region / suppression of viral release by host / PML body organization / SUMO binding / positive regulation of apoptotic process involved in mammary gland involution / fibroblast migration / SMAD protein signal transduction / myeloid cell differentiation / maintenance of protein location in nucleus / endoplasmic reticulum calcium ion homeostasis / branching involved in mammary gland duct morphogenesis / oncogene-induced cell senescence / regulation of double-strand break repair / negative regulation of mitotic cell cycle / Transferases; Acyltransferases; Aminoacyltransferases / Regulation of RUNX1 Expression and Activity / SUMO transferase activity / positive regulation of extrinsic apoptotic signaling pathway / cobalt ion binding / protein-containing complex localization / intrinsic apoptotic signaling pathway in response to oxidative stress / negative regulation of interleukin-1 beta production / entrainment of circadian clock by photoperiod / SUMOylation of ubiquitinylation proteins / SMAD binding / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / protein sumoylation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cell fate commitment / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of signal transduction by p53 class mediator / regulation of cell adhesion / SUMOylation of DNA damage response and repair proteins / protein targeting / response to UV / retinoic acid receptor signaling pathway / Regulation of TP53 Activity through Acetylation / extrinsic apoptotic signaling pathway / positive regulation of defense response to virus by host / response to cytokine / transforming growth factor beta receptor signaling pathway / cellular response to interleukin-4 / Regulation of PTEN localization / negative regulation of angiogenesis / cellular response to leukemia inhibitory factor / response to gamma radiation / circadian regulation of gene expression / DNA damage response, signal transduction by p53 class mediator / negative regulation of cell growth / regulation of circadian rhythm / PML body / nuclear matrix / positive regulation of fibroblast proliferation / Transcriptional regulation of granulopoiesis / intrinsic apoptotic signaling pathway in response to DNA damage / Interferon gamma signaling / protein import into nucleus / HCMV Early Events / cellular senescence / protein-containing complex assembly / early endosome membrane / nuclear membrane / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / response to hypoxia / transcription coactivator activity / chromosome, telomeric region / regulation of cell cycle / protein stabilization / chromatin remodeling / protein heterodimerization activity / negative regulation of cell population proliferation / innate immune response / negative regulation of DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / regulation of DNA-templated transcription / endoplasmic reticulum membrane / nucleolus / protein homodimerization activity / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Protein of unknown function DUF3583 / PML-like, coiled-coil / PML, C-terminal domain / : / ANCHR-like B-box zinc-binding domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, C3HC4 RING-type ...Protein of unknown function DUF3583 / PML-like, coiled-coil / PML, C-terminal domain / : / ANCHR-like B-box zinc-binding domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.06 Å
AuthorsLi, Y. / Ma, X. / Chen, Z. / Wu, H. / Wang, P. / Wu, W. / Cheng, N. / Zeng, L. / Zhang, H. / Cai, X. ...Li, Y. / Ma, X. / Chen, Z. / Wu, H. / Wang, P. / Wu, W. / Cheng, N. / Zeng, L. / Zhang, H. / Cai, X. / Chen, S.J. / Chen, Z. / Meng, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81770142, 81370620, 81570120, 31070645 China
CitationJournal: Nat Commun / Year: 2019
Title: B1 oligomerization regulates PML nuclear body biogenesis and leukemogenesis.
Authors: Li, Y. / Ma, X. / Chen, Z. / Wu, H. / Wang, P. / Wu, W. / Cheng, N. / Zeng, L. / Zhang, H. / Cai, X. / Chen, S.J. / Chen, Z. / Meng, G.
History
DepositionOct 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein PML
B: Protein PML
C: Protein PML
D: Protein PML
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,32613
Polymers23,7674
Non-polymers5599
Water1,47782
1
A: Protein PML
B: Protein PML
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1817
Polymers11,8842
Non-polymers2975
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-20 kcal/mol
Surface area6800 Å2
MethodPISA
2
C: Protein PML
D: Protein PML
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1456
Polymers11,8842
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-7 kcal/mol
Surface area6650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.670, 50.460, 51.430
Angle α, β, γ (deg.)90.00, 101.35, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe PML B1 can form three types of dimer via W157-interface, F158-interface, and N-terminal augmentation. Through combinations of these dimeric interfaces, PML B1 can polymerize into an remarkable B1-network. Via self-self interaction, PML B1 box can form polymer (i.e. N-mer).

-
Components

#1: Protein
Protein PML / Promyelocytic leukemia protein


Mass: 5941.795 Da / Num. of mol.: 4 / Fragment: UNP residues 12-=168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PML / Production host: Escherichia coli (E. coli) / References: UniProt: P29590
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE CORRESPONDS TO THE 5 ISOFORM FOUND IN UNP P29590.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG6K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.282 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2.06→50.4 Å / Num. obs: 11287 / % possible obs: 98 % / Redundancy: 4 % / CC1/2: 0.97 / Rmerge(I) obs: 0.17 / Net I/σ(I): 5.5
Reflection shellResolution: 2.06→2.17 Å / Rmerge(I) obs: 0.69 / Num. unique all: 6697 / Num. unique obs: 1650 / CC1/2: 0.61 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.06→25.23 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 25.41
RfactorNum. reflection% reflection
Rfree0.2265 557 4.94 %
Rwork0.1863 --
obs0.1883 11270 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.06→25.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1609 0 9 82 1700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061649
X-RAY DIFFRACTIONf_angle_d0.9932220
X-RAY DIFFRACTIONf_dihedral_angle_d19.088982
X-RAY DIFFRACTIONf_chiral_restr0.042229
X-RAY DIFFRACTIONf_plane_restr0.005286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.26720.27731230.24562696X-RAY DIFFRACTION99
2.2672-2.5950.25711630.2232687X-RAY DIFFRACTION99
2.595-3.26830.24691280.1932724X-RAY DIFFRACTION99
3.2683-25.23190.19521430.15562606X-RAY DIFFRACTION94
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)
10.0230.03390.00620.4635-0.49630.9740.2710.34670.08460.672-0.53650.06080.25260.9228-0.06260.4172-0.03730.07080.3151-0.09650.34813.81327.647.0359
21.0115-0.0791-0.5641.8732-0.1330.5860.37411.03110.1528-0.644-0.56250.1083-0.0045-1.701-0.02380.28830.093-0.08030.61640.03530.392312.0144.5117-8.0486
32.1547-0.9769-1.47551.2739-0.80932.5508-0.43890.1822-0.17580.3349-0.0270.0520.2785-0.3852-0.73260.2418-0.03180.01430.2146-0.07670.176219.5159-3.2797-3.8012
40.79450.4261-0.30081.6581.87662.7805-1.1926-0.2665-0.97341.93990.48560.34021.78440.40030.20730.580.15330.17420.34070.12380.172518.0609-5.11451.7619
51.41521.2456-1.4612.19850.01940.2079-0.21540.1138-0.170.0030.1222-0.0679-0.02810.0829-0.00640.19870.0103-0.0070.1740.03120.20724.95389.957417.2106
61.48650.6527-0.19561.1868-0.73080.5156-0.1695-0.14070.44510.33710.27480.2924-0.3203-0.12450.00880.24140.00730.01290.15540.01340.21725.421121.477515.032
70.095-0.0632-0.04640.0894-0.0450.0371-0.8675-0.18810.8867-0.2577-0.43640.3952-0.24-0.9157-0.00070.31610.08140.03040.3952-0.07510.37831.8028-2.828319.8949
80.3589-0.2411-0.00130.23020.10010.25810.23440.7197-0.13910.0774-0.2179-0.22190.4983-0.9972-0.00060.2849-0.0053-0.03820.3783-0.03450.2452-13.25660.42419.7068
90.3194-0.1106-0.16490.53410.70410.52250.3180.0447-0.0310.14650.07-0.2290.2064-0.07250.02520.21290.0451-0.04330.2337-0.00420.242-4.95344.534425.632
102.4072-2.4228-1.36423.11922.72234.19560.57940.19330.8121-0.55090.0268-0.9765-0.0864-0.04181.02440.18130.05310.07420.15770.02170.2307-12.61511.898528.2371
110.2606-0.5302-0.31541.69480.03240.73970.4137-0.28440.5404-0.8007-0.1102-0.8023-1.1476-0.4601-0.04570.16740.020.00190.2813-0.10640.472-3.51999.816423.282
120.2209-0.14330.0561.7605-0.80211.72230.4767-0.30660.76010.85-0.867-0.2039-0.1917-0.0699-0.190.18140.05570.09970.074-0.04070.311212.1162.83957.6569
131.8331.5115-1.07163.1378-1.34670.88140.5966-0.8767-0.58360.362-1.0554-0.1342-0.58020.5863-0.15970.193-0.0556-0.04050.33440.04390.268313.7032-7.134316.2772
140.52471.042-0.23621.21250.00730.2307-0.16250.25580.2012-0.43130.11720.09030.2312-0.0520.01410.2147-0.0173-0.04570.23770.01590.16227.9832-9.58867.9072
15-0.0536-0.0589-0.22560.8064-0.5870.6080.227-0.1003-0.12650.0163-0.3543-0.43140.4296-0.02-0.03020.2436-0.01610.03580.1437-0.00030.23198.2946-17.906215.4886
160.196-0.16920.38120.2058-0.27820.55050.12670.0025-0.976-0.7317-0.0255-0.23720.75050.00460.02130.5269-0.0728-0.03830.3258-0.06860.35389.0301-15.13515.0664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 119 through 123 )
2X-RAY DIFFRACTION2chain 'D' and (resid 124 through 137 )
3X-RAY DIFFRACTION3chain 'D' and (resid 138 through 158 )
4X-RAY DIFFRACTION4chain 'D' and (resid 159 through 167 )
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 148 )
6X-RAY DIFFRACTION6chain 'A' and (resid 149 through 167 )
7X-RAY DIFFRACTION7chain 'B' and (resid 119 through 123 )
8X-RAY DIFFRACTION8chain 'B' and (resid 124 through 137 )
9X-RAY DIFFRACTION9chain 'B' and (resid 138 through 148 )
10X-RAY DIFFRACTION10chain 'B' and (resid 149 through 158 )
11X-RAY DIFFRACTION11chain 'B' and (resid 159 through 168 )
12X-RAY DIFFRACTION12chain 'C' and (resid 119 through 128 )
13X-RAY DIFFRACTION13chain 'C' and (resid 129 through 137 )
14X-RAY DIFFRACTION14chain 'C' and (resid 138 through 148 )
15X-RAY DIFFRACTION15chain 'C' and (resid 149 through 158 )
16X-RAY DIFFRACTION16chain 'C' and (resid 159 through 167 )

+
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://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