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- PDB-4dhx: ENY2:GANP complex -

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Basic information

Entry
Database: PDB / ID: 4dhx
TitleENY2:GANP complex
Components
  • 80 kDa MCM3-associated protein
  • Enhancer of yellow 2 transcription factor homolog
KeywordsTRANSPORT PROTEIN/DNA binding Protein / mRNA export / TRANSPORT PROTEIN-DNA binding Protein complex
Function / homology
Function and homology information


: / DUBm complex / transcription export complex 2 / nucleosome organization / nuclear pore nuclear basket / histone H3 acetyltransferase activity / negative regulation of insulin secretion involved in cellular response to glucose stimulus / SAGA complex / poly(A)+ mRNA export from nucleus / somatic hypermutation of immunoglobulin genes ...: / DUBm complex / transcription export complex 2 / nucleosome organization / nuclear pore nuclear basket / histone H3 acetyltransferase activity / negative regulation of insulin secretion involved in cellular response to glucose stimulus / SAGA complex / poly(A)+ mRNA export from nucleus / somatic hypermutation of immunoglobulin genes / mRNA export from nucleus / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / nuclear receptor coactivator activity / transcription elongation by RNA polymerase II / chromosome / HATs acetylate histones / histone binding / nuclear membrane / nucleic acid binding / transcription coactivator activity / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1340 / Germinal-centre associated nuclear protein, MCM3AP domain / Germinal-centre associated nuclear protein, nucleoporin homology domain / Germinal-centre associated nuclear protein, CID domain / MCM3AP, RNA recognition motif / Binding region of GANP to ENY2 / Nucleoporin homology of Germinal-centre associated nuclear protein / MCM3AP domain of GANP / SAC3/GANP/THP3, conserved domain / SAC3/GANP family ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1340 / Germinal-centre associated nuclear protein, MCM3AP domain / Germinal-centre associated nuclear protein, nucleoporin homology domain / Germinal-centre associated nuclear protein, CID domain / MCM3AP, RNA recognition motif / Binding region of GANP to ENY2 / Nucleoporin homology of Germinal-centre associated nuclear protein / MCM3AP domain of GANP / SAC3/GANP/THP3, conserved domain / SAC3/GANP family / ENY2/SUS1 / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 / Serum Albumin; Chain A, Domain 1 / Proteasome component (PCI) domain / PCI domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / RNA-binding domain superfamily / Special / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Germinal-center associated nuclear protein / Transcription and mRNA export factor ENY2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStewart, M. / Jani, D.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Functional and structural characterization of the mammalian TREX-2 complex that links transcription with nuclear messenger RNA export.
Authors: Jani, D. / Lutz, S. / Hurt, E. / Laskey, R.A. / Stewart, M. / Wickramasinghe, V.O.
History
DepositionJan 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 80 kDa MCM3-associated protein
B: Enhancer of yellow 2 transcription factor homolog
C: Enhancer of yellow 2 transcription factor homolog
D: 80 kDa MCM3-associated protein
E: Enhancer of yellow 2 transcription factor homolog
F: Enhancer of yellow 2 transcription factor homolog


Theoretical massNumber of molelcules
Total (without water)63,3186
Polymers63,3186
Non-polymers00
Water4,504250
1
A: 80 kDa MCM3-associated protein
B: Enhancer of yellow 2 transcription factor homolog
C: Enhancer of yellow 2 transcription factor homolog


Theoretical massNumber of molelcules
Total (without water)31,6593
Polymers31,6593
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-61 kcal/mol
Surface area15870 Å2
MethodPISA
2
D: 80 kDa MCM3-associated protein
E: Enhancer of yellow 2 transcription factor homolog
F: Enhancer of yellow 2 transcription factor homolog


Theoretical massNumber of molelcules
Total (without water)31,6593
Polymers31,6593
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-59 kcal/mol
Surface area15030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.592, 76.124, 70.612
Angle α, β, γ (deg.)90.00, 117.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 80 kDa MCM3-associated protein / Protein GANP


Mass: 8555.808 Da / Num. of mol.: 2 / Fragment: ENY2-binding region residues 1163-1235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM3AP, GANP, KIAA0572, MAP80 / Production host: Escherichia coli (E. coli) / References: UniProt: O60318
#2: Protein
Enhancer of yellow 2 transcription factor homolog


Mass: 11551.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ENY2, DC6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NPA8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 11% PEG 8000, 0.2M NaOAc, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 13, 2010 / Details: Osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 37269 / Num. obs: 37269 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Net I/σ(I): 13.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: dev_969)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.884 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 27.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 1863 5 %random
Rwork0.2224 ---
obs0.2239 37246 98.98 %-
all-37269 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.3 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.4746 Å20 Å26.8246 Å2
2--1.0015 Å2-0 Å2
3----6.4761 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 0 250 4306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024090
X-RAY DIFFRACTIONf_angle_d0.5025481
X-RAY DIFFRACTIONf_dihedral_angle_d12.7871613
X-RAY DIFFRACTIONf_chiral_restr0.03649
X-RAY DIFFRACTIONf_plane_restr0.001700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1750.32781780.29783514X-RAY DIFFRACTION99
2.175-2.2620.31141930.2853470X-RAY DIFFRACTION99
2.262-2.36470.27541690.26043564X-RAY DIFFRACTION99
2.3647-2.48920.30591720.24843528X-RAY DIFFRACTION99
2.4892-2.64480.26391870.2453515X-RAY DIFFRACTION99
2.6448-2.84850.30841820.24683549X-RAY DIFFRACTION99
2.8485-3.13410.27031870.24013547X-RAY DIFFRACTION99
3.1341-3.58540.25181890.21663560X-RAY DIFFRACTION99
3.5854-4.50850.21282010.19073538X-RAY DIFFRACTION99
4.5085-19.8840.22152050.19653598X-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)
17.87594.5276.54312.00358.22287.84750.2595-0.4709-0.16940.23560.02290.20991.0032-0.04660.07691.07730.0870.09470.6035-0.26540.5482.0059-49.5622-38.7844
28.6387-7.3682-6.77146.40295.87955.4239-0.53440.1746-0.7913-0.5534-0.0031-0.0063-0.41990.37580.42440.4563-0.05640.11170.4412-0.00940.37790.8438-41.8076-30.7918
32.8153-1.9668-3.02277.23616.94958.76540.0462-0.08560.1132-0.3082-0.0173-0.0055-0.3870.4049-0.01970.25790.02420.00290.21570.04160.2447-4.3124-28.2822-16.9587
47.1772-6.6088-6.2768.54727.09976.05-0.3112-0.2639-0.2951-0.0478-0.02840.4717-0.15230.74780.28420.2625-0.0211-0.01850.1954-0.00240.2606-13.2121-10.43257.2146
55.43094.6103-5.06464.1477-4.45774.8374-0.5646-0.7670.1541-0.4577-0.64460.451.27291.2580.52890.59960.2952-0.03990.8927-0.30260.4484-16.7562-0.627823.8459
67.99945.06624.99164.67722.56333.3569-0.90760.51211.1177-0.44920.27850.2344-0.71730.68680.1720.302-0.1432-0.23411.3547-0.72840.9745-18.64524.568829.7001
74.08823.91450.43035.12032.36218.16380.1297-0.22290.38950.1398-0.13290.0808-1.87410.2645-0.03730.81340.0426-0.10181.115-0.62041.0206-24.23689.889236.7452
85.1632-3.86435.79352.9058-4.34456.5030.1325-0.4463-0.57930.4668-0.5314-0.25861.21430.74580.37260.57480.09850.05350.81240.10360.550711.7691-40.9719-33.5344
96.0822-2.85883.09786.3583.12755.76830.10010.34311.4196-1.23050.0241-1.4789-0.09261.6462-0.09330.4288-0.05770.08780.61680.01130.43979.5501-30.634-36.5605
104.5514-0.0774-4.15629.1771-3.16994.94050.4273-0.08461.32390.2874-0.4251-0.3975-0.9385-0.00810.02140.48040.0079-0.00280.388-0.07850.50172.1105-27.9369-35.2562
114.86830.7299-4.18121.5812-0.96843.59770.06370.53090.0516-0.0742-0.03530.0871-0.3151-0.724-0.01340.2296-0.0157-0.02020.3020.00860.2699-11.5034-28.971-22.4539
125.0036-2.2254-3.48384.38363.03513.1175-0.0321-0.285-0.11320.18780.0005-0.17160.90730.12870.09930.32950.04270.01310.25090.02710.2758-8.3873-30.9092-3.9601
138.7525-1.38695.14298.1176-3.94644.26290.34920.0643-0.4119-0.45030.45030.76050.5331-0.5077-0.65570.4089-0.09520.00650.29-0.00680.4132-11.1996-39.0855-22.4586
143.46653.46190.53125.1346-2.90188.8646-0.57971.254-0.2777-0.59250.3377-0.04960.1484-1.33250.26710.6046-0.0397-0.00680.3598-0.11540.2978-2.0181-37.8051-39.5064
156.53312.86720.34812.0210.32165.41410.09690.1256-0.59160.458-0.0848-0.50190.18790.4704-0.02580.2143-0.0151-0.06210.3277-0.02830.3105-5.0898-6.164811.8298
163.653-4.1102-4.32126.7513.0566.5425-0.1994-0.24380.8310.56010.0081-0.1207-0.38710.13140.06880.3943-0.01360.00290.2555-0.0370.4078-17.25357.687116.7228
173.92550.6907-3.60060.1947-0.53693.5062-0.2085-0.51581.15430.35920.3256-0.0129-0.49350.0246-0.14490.42540.12480.02460.4732-0.23230.5842-30.71375.252929.625
183.001-0.3672-0.37361.76720.84311.9628-0.1487-0.648-0.00930.49740.004-0.40830.27060.64-0.66490.43250.7813-0.2311.2151-0.69360.7052-31.65082.357944.678
199.34671.5624-5.39563.11480.79287.3959-0.6749-0.3781-0.64840.38350.2467-0.26640.9905-0.21540.48320.860.4126-0.08362.3243-0.6820.8395-23.6944-1.173243.3526
204.65881.93345.25835.7154-1.18998.3054-0.3885-1.37340.34090.47161.0429-0.0750.62850.284-0.28160.4070.2489-0.05230.7146-0.19540.4526-26.6939-2.863229.6039
214.0140.7885-5.78952.6522-2.87249.66670.07760.90220.3280.1072-0.05910.076-0.1618-0.4502-0.09190.4149-0.0259-0.14660.3761-0.05860.3849-22.63220.465810.8044
224.0655-2.1099-1.68033.5748-0.85813.05040.34121.131-0.1201-1.9169-0.2644-0.2370.26050.6353-0.15360.67670.05090.01290.4372-0.01450.3018-10.33230.42793.7519
239.2077-4.2849-5.25942.65732.58943.03670.6459-0.71450.32351.6058-1.23470.83680.81280.86710.57380.6960.08050.00961.0885-0.24350.6446-19.453223.932411.7243
241.5382-3.2471-4.22517.80119.10138.733-0.3458-0.2601-0.1320.22670.14330.39640.03880.18920.29280.53570.235-0.02550.472-0.07460.3366-10.86020.7767-19.8377
257.7334-3.1998-3.87899.12283.60713.0307-0.84870.4162-1.58670.1705-0.17111.71190.6869-1.12871.01560.3420.01590.07920.3348-0.04090.48783.8698-27.2293-52.7022
269.3466-5.40865.43129.4027-6.38035.0834-0.97-0.83130.02181.58551.1209-1.18440.3819-0.2082-0.26551.05210.2109-0.06640.5553-0.07630.627-28.996518.508314.3677
279.2907-1.4963-6.94142.04222.04448.9453-0.0221-0.50210.0559-0.03380.4794-0.33450.80190.595-0.21860.26040.1144-0.0670.3543-0.12150.3375-23.032221.9908-4.1673
287.4288-4.5736-0.63283.685-0.20990.41670.10860.48770.6395-0.3050.4406-0.91650.17380.9256-0.11580.49190.0973-0.08521.0051-0.27650.5034-6.323612.263-13.0674
294.8008-0.3092-0.01358.10540.92324.6980.1692-0.69550.17910.54530.1658-0.54840.34170.8202-0.26510.34380.1065-0.01050.793-0.10260.3798-7.907811.8818-5.0442
302.0211.4137-2.96215.1847-5.76368.88660.95510.09491.08330.40110.85380.7419-1.5195-0.3026-0.55370.5097-0.00390.10220.4513-0.330.7962-25.903229.51466.5161
319.38475.4415.46987.84384.66273.70390.1912-0.6320.10150.4244-0.16180.2259-0.0634-0.66680.01360.41720.1220.11960.42040.05290.3647-10.9815-17.523-30.9978
322.76181.52961.27243.933-1.72642.7478-0.1016-0.4705-0.1482-0.10740.079-0.02610.23820.15840.07180.2543-0.04810.00460.33290.01120.3661-8.2221-17.4512-49.7715
337.1259-4.962-1.93174.11230.17922.65750.61220.0067-0.1994-0.3413-0.15360.36030.06160.0366-0.51580.3863-0.0440.03990.3351-0.06450.35325.1795-18.0181-56.6451
342.15-0.4528-0.31271.7565-2.77018.1475-0.6318-0.0232-0.12860.03610.3232-0.27830.81520.56550.28680.420.07170.01790.3124-0.0410.342216.959-27.0993-57.5012
357.3481-5.0506-1.73674.60362.87633.0229-0.5729-0.84310.19620.86560.5558-0.45420.36010.95110.03840.38180.02120.03590.3951-0.00760.303910.7613-21.3067-48.2927
362.247-0.80921.55575.14880.73232.29020.53340.98010.5158-0.525-0.14090.5885-0.7862-0.8624-0.56020.38620.1021-0.05040.3733-0.00160.4337-4.4854-7.7872-46.227
378.9631-5.2444-5.953.39563.46134.4001-0.43310.267-1.22310.0718-0.4090.8295-0.5786-1.65210.7460.56230.28360.14940.68470.02740.743-16.9778-10.2381-36.6456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1162:1167)
2X-RAY DIFFRACTION2(chain A and resid 1168:1174)
3X-RAY DIFFRACTION3(chain A and resid 1175:1195)
4X-RAY DIFFRACTION4(chain A and resid 1196:1216)
5X-RAY DIFFRACTION5(chain A and resid 1217:1221)
6X-RAY DIFFRACTION6(chain A and resid 1222:1226)
7X-RAY DIFFRACTION7(chain A and resid 1227:1233)
8X-RAY DIFFRACTION8(chain B and resid 9:17)
9X-RAY DIFFRACTION9(chain B and resid 18:22)
10X-RAY DIFFRACTION10(chain B and resid 23:28)
11X-RAY DIFFRACTION11(chain B and resid 29:51)
12X-RAY DIFFRACTION12(chain B and resid 52:72)
13X-RAY DIFFRACTION13(chain B and resid 73:83)
14X-RAY DIFFRACTION14(chain B and resid 84:99)
15X-RAY DIFFRACTION15(chain C and resid 7:24)
16X-RAY DIFFRACTION16(chain C and resid 25:39)
17X-RAY DIFFRACTION17(chain C and resid 40:53)
18X-RAY DIFFRACTION18(chain C and resid 54:60)
19X-RAY DIFFRACTION19(chain C and resid 61:66)
20X-RAY DIFFRACTION20(chain C and resid 67:79)
21X-RAY DIFFRACTION21(chain C and resid 80:90)
22X-RAY DIFFRACTION22(chain C and resid 91:99)
23X-RAY DIFFRACTION23(chain D and resid 1166:1174)
24X-RAY DIFFRACTION24(chain D and resid 1175:1220)
25X-RAY DIFFRACTION25(chain D and resid 1221:1234)
26X-RAY DIFFRACTION26(chain E and resid 9:23)
27X-RAY DIFFRACTION27(chain E and resid 24:42)
28X-RAY DIFFRACTION28(chain E and resid 43:58)
29X-RAY DIFFRACTION29(chain E and resid 59:82)
30X-RAY DIFFRACTION30(chain E and resid 83:100)
31X-RAY DIFFRACTION31(chain F and resid 9:26)
32X-RAY DIFFRACTION32(chain F and resid 27:40)
33X-RAY DIFFRACTION33(chain F and resid 41:50)
34X-RAY DIFFRACTION34(chain F and resid 51:63)
35X-RAY DIFFRACTION35(chain F and resid 64:77)
36X-RAY DIFFRACTION36(chain F and resid 78:89)
37X-RAY DIFFRACTION37(chain F and resid 90:99)

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  • 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

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