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- PDB-4afl: The crystal structure of the ING4 dimerization domain reveals the... -

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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


DNA replication-dependent chromatin disassembly / regulation of DNA biosynthetic process / negative regulation of growth / intermediate filament cytoskeleton / histone H3K4me3 reader activity / regulation of cell cycle G2/M phase transition / positive regulation of DNA damage response, signal transduction by p53 class mediator / protein acetylation / : / histone acetyltransferase complex ...DNA replication-dependent chromatin disassembly / regulation of DNA biosynthetic process / negative regulation of growth / intermediate filament cytoskeleton / histone H3K4me3 reader activity / regulation of cell cycle G2/M phase transition / positive regulation of DNA damage response, signal transduction by p53 class mediator / protein acetylation / : / histone acetyltransferase complex / regulation of cell growth / HATs acetylate histones / transcription coactivator activity / regulation of cell cycle / positive regulation of apoptotic process / chromatin remodeling / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / apoptotic process / regulation of DNA-templated transcription / zinc ion binding / nucleoplasm / 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. / Helix non-globular / Zinc finger PHD-type profile. ...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. / Helix non-globular / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / 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
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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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.

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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

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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)

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