[English] 日本語
Yorodumi
- PDB-4ptb: Crystal structure of human SP100 PHD-Bromodomain in the free state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ptb
TitleCrystal structure of human SP100 PHD-Bromodomain in the free state
ComponentsNuclear autoantigen Sp-100
KeywordsTRANSCRIPTION / Nuclear autoantigen Sp-100 / Nuclear dot-associated Sp100 protein / Speckled 100 kDa
Function / homology
Function and homology information


regulation of Fas signaling pathway / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / negative regulation of protein export from nucleus / negative regulation of endothelial cell migration / regulation of extrinsic apoptotic signaling pathway via death domain receptors / type I interferon-mediated signaling pathway / response to type II interferon ...regulation of Fas signaling pathway / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / negative regulation of protein export from nucleus / negative regulation of endothelial cell migration / regulation of extrinsic apoptotic signaling pathway via death domain receptors / type I interferon-mediated signaling pathway / response to type II interferon / negative regulation of DNA binding / DNA damage response, signal transduction by p53 class mediator / retinoic acid receptor signaling pathway / regulation of angiogenesis / SUMOylation of DNA damage response and repair proteins / type II interferon-mediated signaling pathway / response to retinoic acid / telomere maintenance / nuclear periphery / response to cytokine / negative regulation of DNA-binding transcription factor activity / PML body / kinase binding / positive regulation of DNA-binding transcription factor activity / Interferon gamma signaling / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / protein dimerization activity / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / protein domain specific binding / negative regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Nuclear body protein Sp140 / HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily ...Nuclear body protein Sp140 / HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / 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 / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SP100 nuclear antigen / Nuclear autoantigen Sp-100
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsTallant, C. / Nunez-Alonso, G. / Savitsky, P. / Newman, J. / Krojer, T. / Szykowska, A. / Burgess-Brown, N. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. ...Tallant, C. / Nunez-Alonso, G. / Savitsky, P. / Newman, J. / Krojer, T. / Szykowska, A. / Burgess-Brown, N. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S.
CitationJournal: To be Published
Title: Crystal structure of human SP100 PHD-Bromodomain in the free state
Authors: Tallant, C. / Nunez-Alonso, G. / Savitsky, P. / Newman, J. / Krojer, T. / Szykowska, A. / Burgess-Brown, N. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S.
History
DepositionMar 10, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nuclear autoantigen Sp-100
B: Nuclear autoantigen Sp-100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,70211
Polymers42,9972
Non-polymers7059
Water3,603200
1
A: Nuclear autoantigen Sp-100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9496
Polymers21,4991
Non-polymers4505
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nuclear autoantigen Sp-100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7545
Polymers21,4991
Non-polymers2554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.520, 45.183, 83.188
Angle α, β, γ (deg.)90.00, 102.21, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Nuclear autoantigen Sp-100


Mass: 21498.564 Da / Num. of mol.: 2 / Fragment: UNP residues 74-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SP100 / Plasmid: pSUMO-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: H0Y4R8, UniProt: P23497*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 22% PEG 20000, 0.1M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.282 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 1.6→28.37 Å / Num. all: 58158 / Num. obs: 58158 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 19.26 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.028 / Net I/σ(I): 23.3
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value
1.6-1.693.450.2914.65175390.291
1.69-1.813.480.1757.37169160.175
1.81-1.963.50.10111.54159150.101
1.96-2.143.550.06316.99147490.063
2.14-2.393.380.04721.87134270.047
2.39-2.763.50.04125.86119670.041
2.76-3.373.260.03927.63100360.039
3.37-4.733.350.03730.4978350.037
4.73-28.373.320.04130.7443820.041

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→27.72 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.337 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19229 2950 5.1 %RANDOM
Rwork0.17303 ---
all0.17402 55205 --
obs0.17402 55205 94.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.806 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20.38 Å2
2---0.3 Å2-0 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2866 0 32 200 3098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193038
X-RAY DIFFRACTIONr_bond_other_d0.0010.022826
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9394088
X-RAY DIFFRACTIONr_angle_other_deg0.80436520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.275359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80223.72164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54215557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.491525
X-RAY DIFFRACTIONr_chiral_restr0.0830.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213442
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02775
X-RAY DIFFRACTIONr_mcbond_it1.5641.9141409
X-RAY DIFFRACTIONr_mcbond_other1.5561.9121408
X-RAY DIFFRACTIONr_mcangle_it2.5042.8561765
X-RAY DIFFRACTIONr_mcangle_other2.5052.8581766
X-RAY DIFFRACTIONr_scbond_it2.592.2611629
X-RAY DIFFRACTIONr_scbond_other2.5892.2611629
X-RAY DIFFRACTIONr_scangle_other4.1273.272320
X-RAY DIFFRACTIONr_long_range_B_refined5.73215.9063624
X-RAY DIFFRACTIONr_long_range_B_other5.68915.5413527
LS refinement shellResolution: 1.598→1.639 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.18 212 -
Rwork0.184 3848 -
obs--89.55 %
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)
10.3951-0.2914-0.03120.6138-0.04110.27240.07260.04950.0044-0.0094-0.06980.00030.0251-0.0093-0.00280.04080.0187-0.00340.02370.00070.015726.12873.854516.319
20.746-0.00570.24320.21280.1090.33420.110.04110.0471-0.0274-0.0722-0.0682-0.0153-0.0703-0.03770.03260.03440.01520.05650.02290.0283-2.298724.064119.3789
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A701 - 878
2X-RAY DIFFRACTION2B701 - 875

+
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