[English] 日本語
Yorodumi
- PDB-4afl: The crystal structure of the ING4 dimerization domain reveals the... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4afl
TitleThe crystal structure of the ING4 dimerization domain reveals the functional organization of the ING family of chromatin binding proteins.
ComponentsINHIBITOR OF GROWTH PROTEIN 4
KeywordsCELL CYCLE / TUMOUR SUPPRESSOR / CHROMATIN REMODELLING
Function / homology
Function and homology information


regulation of DNA biosynthetic process / DNA replication-dependent chromatin disassembly / negative regulation of growth / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / regulation of cell cycle G2/M phase transition / intermediate filament cytoskeleton / protein acetylation / histone acetyltransferase complex / methylated histone binding / regulation of cell growth ...regulation of DNA biosynthetic process / DNA replication-dependent chromatin disassembly / negative regulation of growth / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / regulation of cell cycle G2/M phase transition / intermediate filament cytoskeleton / protein acetylation / histone acetyltransferase complex / methylated histone binding / regulation of cell growth / HATs acetylate histones / transcription coactivator activity / regulation of cell cycle / chromatin remodeling / cell cycle / positive regulation of apoptotic process / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / apoptotic process / regulation of DNA-templated transcription / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
Helix Hairpins - #1740 / Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / Helix Hairpins / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger ...Helix Hairpins - #1740 / Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / Helix Hairpins / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Helix non-globular / Zinc finger, PHD-type / PHD zinc finger / Special / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Inhibitor of growth protein 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.275 Å
AuthorsCulurgioni, S. / Munoz, I.G. / Moreno, A. / Palacios, A. / Villate, M. / Palmero, I. / Montoya, G. / Blanco, F.J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal Structure of Inhibitor of Growth 4 (Ing4) Dimerization Domain Reveals Functional Organization of Ing Family of Chromatin-Binding Proteins.
Authors: Culurgioni, S. / Munoz, I.G. / Moreno, A. / Palacios, A. / Villate, M. / Palmero, I. / Montoya, G. / Blanco, F.J.
History
DepositionJan 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Other
Revision 1.2Jul 11, 2012Group: Other

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: INHIBITOR OF GROWTH PROTEIN 4
B: INHIBITOR OF GROWTH PROTEIN 4
C: INHIBITOR OF GROWTH PROTEIN 4
D: INHIBITOR OF GROWTH PROTEIN 4
E: INHIBITOR OF GROWTH PROTEIN 4
F: INHIBITOR OF GROWTH PROTEIN 4


Theoretical massNumber of molelcules
Total (without water)74,4076
Polymers74,4076
Non-polymers00
Water3,351186
1
A: INHIBITOR OF GROWTH PROTEIN 4
C: INHIBITOR OF GROWTH PROTEIN 4


Theoretical massNumber of molelcules
Total (without water)24,8022
Polymers24,8022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-37.6 kcal/mol
Surface area12230 Å2
MethodPISA
2
B: INHIBITOR OF GROWTH PROTEIN 4
F: INHIBITOR OF GROWTH PROTEIN 4


Theoretical massNumber of molelcules
Total (without water)24,8022
Polymers24,8022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-37.7 kcal/mol
Surface area10910 Å2
MethodPISA
3
D: INHIBITOR OF GROWTH PROTEIN 4
E: INHIBITOR OF GROWTH PROTEIN 4


Theoretical massNumber of molelcules
Total (without water)24,8022
Polymers24,8022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-39.1 kcal/mol
Surface area11610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.450, 186.600, 62.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.4458, -0.4793, 0.756), (0.1531, 0.7913, 0.5919), (-0.8819, 0.3796, -0.2794)14.5357, 8.4528, 79.7095
3given(1), (1), (1)
4given(-0.4458, -0.4793, 0.756), (0.1531, 0.7913, 0.5919), (-0.8819, 0.3796, -0.2794)14.5357, 8.4528, 79.7095
5given(0.9585, 0.2826, 0.0377), (0.2827, -0.9592, 0.0042), (0.0374, 0.0067, -0.9993)-14.009, 81.9654, 99.6181
6given(0.9585, 0.2826, 0.0377), (0.2827, -0.9592, 0.0042), (0.0374, 0.0067, -0.9993)-14.009, 81.9654, 99.6181
7given(0.4699, 0.0345, -0.882), (0.4679, -0.857, 0.2157), (-0.7485, -0.5141, -0.4189)53.9293, 28.0401, 116.5614
8given(0.4699, 0.0345, -0.882), (0.4679, -0.857, 0.2157), (-0.7485, -0.5141, -0.4189)53.9293, 28.0401, 116.5614
9given(0.5465, -0.3045, -0.7801), (-0.2634, 0.8217, -0.5053), (0.7949, 0.4817, 0.3689)50.5162, 72.0595, -14.2413
10given(0.5465, -0.3045, -0.7801), (-0.2634, 0.8217, -0.5053), (0.7949, 0.4817, 0.3689)50.5162, 72.0595, -14.2413
11given(-0.4323, -0.1721, 0.8852), (-0.3114, -0.8928, -0.3256), (0.8463, -0.4164, 0.3323)5.1225, 78.7597, 20.86
12given(-0.4323, -0.1721, 0.8852), (-0.3114, -0.8928, -0.3256), (0.8463, -0.4164, 0.3323)5.1225, 78.7597, 20.86

-
Components

#1: Protein
INHIBITOR OF GROWTH PROTEIN 4 / P29ING4


Mass: 12401.243 Da / Num. of mol.: 6 / Fragment: N-TERMINAL DIMERIZATION DOMAIN, RESIDUES 2-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UNL4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.66 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 7.5
Details: 24% PEG 3350, 0.1 M BISTRIS- PROPANE PH:7.5, 0.4 M SODIUM NITRATE, 10% OPTISALT SOLUTION 6, SILVER BULLET ADDITIVE 3.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2009
RadiationMonochromator: SILICON (1 1 1) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.27→47.09 Å / Num. obs: 34302 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 35.92 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.1
Reflection shellResolution: 2.27→2.4 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.1 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.275→44.688 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 25.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 1735 5.1 %
Rwork0.2046 --
obs0.2073 34302 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.912 Å2 / ksol: 0.349 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.1314 Å20 Å20 Å2
2---2.6657 Å20 Å2
3----2.8637 Å2
Refinement stepCycle: LAST / Resolution: 2.275→44.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4692 0 0 186 4878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084757
X-RAY DIFFRACTIONf_angle_d0.9956384
X-RAY DIFFRACTIONf_dihedral_angle_d16.5971816
X-RAY DIFFRACTIONf_chiral_restr0.061709
X-RAY DIFFRACTIONf_plane_restr0.004834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.275-2.35630.37161460.26972815X-RAY DIFFRACTION87
2.3563-2.45070.30791700.24933260X-RAY DIFFRACTION100
2.4507-2.56220.31811940.22773242X-RAY DIFFRACTION100
2.5622-2.69720.3171530.21453327X-RAY DIFFRACTION100
2.6972-2.86620.29081710.21333254X-RAY DIFFRACTION100
2.8662-3.08750.26031740.2193281X-RAY DIFFRACTION100
3.0875-3.39810.24551690.20843303X-RAY DIFFRACTION100
3.3981-3.88950.23311740.18383338X-RAY DIFFRACTION100
3.8895-4.89940.2021850.16043322X-RAY DIFFRACTION100
4.8994-44.69680.26141990.22263425X-RAY DIFFRACTION99
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)
10.8882-0.2254-1.00370.01221.17697.218-0.1218-0.017-0.01720.1245-0.0275-0.12410.2601-0.46560.09830.2883-0.04290.01850.11020.02250.190115.054638.214646.7171
2-0.26410.4027-0.54621.1164-3.43395.31-0.1135-0.1625-0.1467-0.0478-0.4235-0.18380.33110.62460.27940.39480.0126-0.02030.30590.02130.24320.784942.846647.9912
34.46280.9272.1455.81634.4613.9047-0.4559-1.3605-0.7851.4099-0.05510.0203-0.9105-0.26750.18820.3739-0.0533-0.11150.57710.1330.231143.0109-3.473341.712
49.3615-5.43964.22564.0826-3.34882.8509-0.287-0.05930.730.1855-0.0085-0.3244-0.1481-0.07310.23840.2469-0.0487-0.05250.20290.00170.235133.44213.165224.3535
53.4987-1.10143.87440.8062-1.30354.22930.2482-0.3863-0.1841-0.17880.12590.14350.3858-0.3481-0.28040.2346-0.0469-0.02420.38950.06880.30526.924913.672930.8926
63.63564.4461-3.15229.33281.28479.53880.1739-0.6793-0.91030.41470.6445-1.74440.82550.94590.12620.40690.0757-0.0120.38510.16530.506125.53755.699972.15
7-0.0938-0.03670.13210.1971.06132.27930.02790.1125-0.1786-0.0034-0.1150.03190.3203-0.11340.13790.27170.02480.00580.3405-0.04580.250610.644148.659847.8582
80.1335-0.62251.80380.5083-2.65975.2799-0.46970.03120.24860.1639-0.419-0.4106-0.50930.05740.460.35860.05790.0380.37040.05910.271320.3647.103853.0369
96.51084.3775-5.28665.5163-1.9895.3025-0.6564-0.1704-1.2935-0.56080.4125-0.0393-0.1231-0.85770.29760.1768-0.0263-0.02460.45480.0790.396958.619337.357462.7752
106.40695.99442.57595.04412.33612.80920.3347-0.08570.26110.4006-0.43620.42360.2644-0.19810.16480.22550.02180.04830.2207-0.03090.405534.640923.990366.9366
118.8285.00837.01263.08992.83165.0788-0.04450.80820.7062-0.1394-0.07180.1718-0.07010.44780.25190.28840.0280.01280.30080.02990.316743.581722.107161.495
125.175-2.64581.76616.7352-3.60143.15750.02270.4771-0.4051-0.9051-0.3471-0.6742-0.0256-0.37390.0458-0.21721.1964-0.4737-0.70870.59990.129229.686-2.849751.0429
138.14195.52574.58535.24113.63525.02330.2625-0.41440.34390.4634-0.28470.24350.06730.01670.04780.3204-0.02340.03820.28340.04890.251939.459415.587971.3571
145.92822.93626.6630.82452.37736.14190.14580.5906-0.1316-0.01980.0542-0.11180.3130.5277-0.16020.23180.0087-0.04040.37790.01140.290241.070915.217660.9021
157.6622-4.78282.60342.8692-1.36422.02920.50350.1940.1553-0.1025-0.2825-0.07470.0814-0.0069-0.12430.3706-0.0895-0.08260.20080.07880.349329.407125.01428.2621
165.0171-4.110.79357.7577-2.96986.2676-0.12930.7705-0.2108-0.9284-0.18920.98231.2912-0.65740.42090.45980.13960.01750.63670.03040.716956.993810.802434.2323
173.4751-1.07832.48321.5334-0.05172.35670.0938-0.240.86690.1153-0.02450.0608-0.0073-0.1264-0.02960.3074-0.0321-0.12760.23130.06840.269328.820818.348435.0345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 3:57)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 58:104)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 4:13)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 14:51)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 52:101)
6X-RAY DIFFRACTION6CHAIN C AND (RESSEQ 4:13)
7X-RAY DIFFRACTION7CHAIN C AND (RESSEQ 14:57)
8X-RAY DIFFRACTION8CHAIN C AND (RESSEQ 58:105)
9X-RAY DIFFRACTION9CHAIN D AND (RESSEQ 5:13)
10X-RAY DIFFRACTION10CHAIN D AND (RESSEQ 14:59)
11X-RAY DIFFRACTION11CHAIN D AND (RESSEQ 60:103)
12X-RAY DIFFRACTION12CHAIN E AND (RESSEQ 4:13)
13X-RAY DIFFRACTION13CHAIN E AND (RESSEQ 14:57)
14X-RAY DIFFRACTION14CHAIN E AND (RESSEQ 58:104)
15X-RAY DIFFRACTION15CHAIN F AND (RESSEQ 10:48)
16X-RAY DIFFRACTION16CHAIN F AND (RESSEQ 49:57)
17X-RAY DIFFRACTION17CHAIN F AND (RESSEQ 58:103)

+
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