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- PDB-3g36: Crystal structure of the human DPY-30-like C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3g36
TitleCrystal structure of the human DPY-30-like C-terminal domain
ComponentsProtein dpy-30 homolog
KeywordsNUCLEAR PROTEIN / X-type four-helix bundle / Nucleus
Function / homology
Function and homology information


MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / endosomal transport / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / transcription initiation-coupled chromatin remodeling / trans-Golgi network / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / endosomal transport / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / transcription initiation-coupled chromatin remodeling / trans-Golgi network / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Golgi apparatus / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / : / Sdc1/DPY30 / Dpy-30 motif / Dpy-30 motif / cAMP-dependent Protein Kinase, Chain A / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / HEXANE-1,6-DIOL / Protein dpy-30 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsWang, X. / Lou, Z. / Bartlam, M. / Rao, Z.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of the C-terminal domain of human DPY-30-like protein: A component of the histone methyltransferase complex
Authors: Wang, X. / Lou, Z. / Dong, X. / Yang, W. / Peng, Y. / Yin, B. / Gong, Y. / Yuan, J. / Zhou, W. / Bartlam, M. / Peng, X. / Rao, Z.
History
DepositionFeb 2, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 4, 2019Group: Data collection / Derived calculations / Category: reflns / reflns_shell / struct_conn
Item: _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein dpy-30 homolog
B: Protein dpy-30 homolog
C: Protein dpy-30 homolog
D: Protein dpy-30 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8148
Polymers25,2334
Non-polymers5814
Water6,503361
1
A: Protein dpy-30 homolog
C: Protein dpy-30 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0795
Polymers12,6162
Non-polymers4633
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-23 kcal/mol
Surface area6350 Å2
MethodPISA
2
B: Protein dpy-30 homolog
D: Protein dpy-30 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7353
Polymers12,6162
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-24 kcal/mol
Surface area6540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.401, 51.388, 51.388
Angle α, β, γ (deg.)90.00, 107.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Protein dpy-30 homolog / Dpy-30-like protein


Mass: 6308.166 Da / Num. of mol.: 4 / Fragment: C-terminal domain, UNI residues 45-99 / Mutation: L69M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPY-30-like / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9C005

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Non-polymers , 5 types, 365 molecules

#2: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris, 28% PEG-MME 2000, 3% 1,6 hexanediol (additive), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 51431 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.7
Reflection shellResolution: 1.2→1.3 Å / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 4.1 / % possible all: 79.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.5.0044refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.2→43.16 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.682 / SU ML: 0.034 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2449 5 %RANDOM
Rwork0.195 46787 --
obs0.197 49236 76.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 398.02 Å2 / Biso mean: 17.958 Å2 / Biso min: 3.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20.09 Å2
2---0.01 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.2→43.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1624 0 32 361 2017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221684
X-RAY DIFFRACTIONr_angle_refined_deg1.3532.0352285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1815201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44325.36269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65115293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.14158
X-RAY DIFFRACTIONr_chiral_restr0.1030.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0221224
X-RAY DIFFRACTIONr_mcbond_it0.8731.51037
X-RAY DIFFRACTIONr_mcangle_it1.63821688
X-RAY DIFFRACTIONr_scbond_it2.3333647
X-RAY DIFFRACTIONr_scangle_it3.7814.5597
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 28 -
Rwork0.358 505 -
all-533 -
obs--11.19 %
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)
10.36170.0791-0.00310.1956-0.00940.0777-0.0161-0.00710.01230.00850.00870.0146-0.00970.00440.00740.00310.00010.00060.00120.00010.00545.096813.604616.7101
20.2060.0050.04090.05410.04550.1853-0.0054-0.00340.01010.00330.00070.0045-0.0051-0.00550.00460.00070.00040.00010.0003-0.00010.0008-3.252-1.168913.803
30.09380.0475-0.07590.2107-0.0120.1088-0.01080.00280.0196-0.03710.01250.0184-0.01770.0053-0.00170.0176-0.0052-0.01010.00160.00290.00883.177119.94189.5333
40.21260.1024-0.02490.10660.00190.1243-0.0002-0.0016-0.0121-0.00180.0006-0.01240.01170.0003-0.00050.0013-0.00010.00020.0001-0.00010.00152.8562-7.5069.3029
511.9787-15.5474-0.284423.41892.37891.25360.32680.1706-0.0553-0.1458-0.0717-0.3410.16530.089-0.2550.06210.0257-0.03640.0992-0.01670.05319.25854.045416.8801
658.4-3.4586-10.44178.238612.50919.46610.91670.74980.46940.1845-0.4079-0.31470.1892-0.6717-0.50880.0254-0.00050.00070.02680.01820.0157.47333.76927.0321
768.285647.2058-20.5042113.886257.80569.92211.1765-1.36452.69971.1165-1.22772.8442-0.09040.16820.05120.043-0.06470.05030.134-0.07230.13186.138111.44017.9435
80-0-0.00010.00010.00010.00020.00240.0023-0.0001-0.00490.00120.0006-0.0048-0.0064-0.00360.35370.002-0.04340.49760.25450.64851.81911.04765.6932
90.14750.11450.03650.24370.0370.11490.0003-0.00170.00380.00360.00590.0031-0.0010.0026-0.00620.00010.00010.00010.0004-0.00020.00062.26855.692713.186
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A47 - 97
2X-RAY DIFFRACTION2B46 - 96
3X-RAY DIFFRACTION3C46 - 96
4X-RAY DIFFRACTION4D46 - 96
5X-RAY DIFFRACTION5D1
6X-RAY DIFFRACTION6A1
7X-RAY DIFFRACTION7A100
8X-RAY DIFFRACTION8C1
9X-RAY DIFFRACTION9A3 - 465
10X-RAY DIFFRACTION9C8 - 464
11X-RAY DIFFRACTION9B4 - 451
12X-RAY DIFFRACTION9D2 - 466

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