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- PDB-5fd3: Structure of Lin54 tesmin domain bound to DNA -

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Basic information

Entry
Database: PDB / ID: 5fd3
TitleStructure of Lin54 tesmin domain bound to DNA
Components
  • DNA (5'-D(*CP*AP*GP*TP*TP*TP*CP*AP*AP*AP*CP*TP*C)-3')
  • DNA (5'-D(*GP*AP*GP*TP*TP*TP*GP*AP*AP*AP*CP*T)-3')
  • Protein lin-54 homolog
KeywordsTRANSCRIPTION/DNA / transcription factor / tesmin domain / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


transcription regulatory region nucleic acid binding / RNA polymerase II transcription repressor complex / nucleosome organization / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Transcription of E2F targets under negative control by DREAM complex / Polo-like kinase mediated events / G1/S-Specific Transcription / minor groove of adenine-thymine-rich DNA binding / G0 and Early G1 / Cyclin E associated events during G1/S transition ...transcription regulatory region nucleic acid binding / RNA polymerase II transcription repressor complex / nucleosome organization / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Transcription of E2F targets under negative control by DREAM complex / Polo-like kinase mediated events / G1/S-Specific Transcription / minor groove of adenine-thymine-rich DNA binding / G0 and Early G1 / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / regulation of DNA-templated transcription / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
CRC domain / Lin-54 family / Tesmin/TSO1-like CXC domain, cysteine-rich domain / CRC domain profile. / Tesmin/TSO1-like CXC domain / Tesmin/TSO1-like CXC domain
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein lin-54 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsMarceau, A.H. / Felthousen, J.G. / Goetsch, P.D. / Lee, H. / Tripathi, S.M. / Strome, S. / Litovchick, L. / Rubin, S.M.
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis for LIN54 recognition of CHR elements in cell cycle-regulated promoters.
Authors: Marceau, A.H. / Felthousen, J.G. / Goetsch, P.D. / Iness, A.N. / Lee, H.W. / Tripathi, S.M. / Strome, S. / Litovchick, L. / Rubin, S.M.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein lin-54 homolog
B: Protein lin-54 homolog
C: DNA (5'-D(*GP*AP*GP*TP*TP*TP*GP*AP*AP*AP*CP*T)-3')
D: DNA (5'-D(*CP*AP*GP*TP*TP*TP*CP*AP*AP*AP*CP*TP*C)-3')
H: DNA (5'-D(*GP*AP*GP*TP*TP*TP*GP*AP*AP*AP*CP*T)-3')
I: DNA (5'-D(*CP*AP*GP*TP*TP*TP*CP*AP*AP*AP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,67218
Polymers45,8876
Non-polymers78512
Water1,00956
1
A: Protein lin-54 homolog
H: DNA (5'-D(*GP*AP*GP*TP*TP*TP*GP*AP*AP*AP*CP*T)-3')
I: DNA (5'-D(*CP*AP*GP*TP*TP*TP*CP*AP*AP*AP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3369
Polymers22,9443
Non-polymers3926
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-28 kcal/mol
Surface area10740 Å2
MethodPISA
2
B: Protein lin-54 homolog
C: DNA (5'-D(*GP*AP*GP*TP*TP*TP*GP*AP*AP*AP*CP*T)-3')
D: DNA (5'-D(*CP*AP*GP*TP*TP*TP*CP*AP*AP*AP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3369
Polymers22,9443
Non-polymers3926
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-28 kcal/mol
Surface area10700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.320, 53.880, 67.120
Angle α, β, γ (deg.)98.400, 102.530, 106.570
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain C
22chain H
13chain D
23chain I

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGHISHISchain AAA522 - 64311 - 132
21ARGARGZNZNchain BBB - R522 - 70611
12DGDGDTDTchain CCC1 - 121 - 12
22DGDGDTDTchain HHE1 - 121 - 12
13DCDCDCDCchain DDD1 - 131 - 13
23DCDCDCDCchain IIF1 - 131 - 13

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Protein lin-54 homolog / CXC domain-containing protein 1


Mass: 15331.646 Da / Num. of mol.: 2 / Fragment: tesmin domain (UNP residues 515-646)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIN54, CXCDC1, KIAA2037 / Plasmid: pGEV / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6MZP7
#2: DNA chain DNA (5'-D(*GP*AP*GP*TP*TP*TP*GP*AP*AP*AP*CP*T)-3')


Mass: 3701.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*AP*GP*TP*TP*TP*CP*AP*AP*AP*CP*TP*C)-3')


Mass: 3910.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.83 Å3/Da / Density % sol: 56.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 21% PEG 3350, 310 mM Magnesium Chloride Hexahydrate

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Data collection

DiffractionMean temperature: 75 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03318 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 18, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 2.42→63.88 Å / Num. obs: 18229 / % possible obs: 95.1 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.86
Reflection shellResolution: 2.42→2.55 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.2 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RKH

4rkh


Resolution: 2.42→36 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 30.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 908 5 %
Rwork0.1806 17237 -
obs0.1836 18145 94.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.38 Å2 / Biso mean: 61.4305 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.42→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1657 979 12 56 2704
Biso mean--49.82 48.7 -
Num. residues----266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012773
X-RAY DIFFRACTIONf_angle_d1.213925
X-RAY DIFFRACTIONf_chiral_restr0.05424
X-RAY DIFFRACTIONf_plane_restr0.006345
X-RAY DIFFRACTIONf_dihedral_angle_d23.321110
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A916X-RAY DIFFRACTION7.179TORSIONAL
12B916X-RAY DIFFRACTION7.179TORSIONAL
21C232X-RAY DIFFRACTION7.179TORSIONAL
22H232X-RAY DIFFRACTION7.179TORSIONAL
31D212X-RAY DIFFRACTION7.179TORSIONAL
32I212X-RAY DIFFRACTION7.179TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4201-2.57170.3541560.27392859X-RAY DIFFRACTION94
2.5717-2.77020.31251370.24852863X-RAY DIFFRACTION95
2.7702-3.04880.32521420.2512912X-RAY DIFFRACTION95
3.0488-3.48970.30521520.20122814X-RAY DIFFRACTION94
3.4897-4.39540.20181690.15192918X-RAY DIFFRACTION96
4.3954-360.18621520.14172871X-RAY DIFFRACTION95
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)
10.952-0.1770.33070.2319-0.17850.1249-0.0473-0.1839-0.2397-0.0074-0.006-0.3818-0.1445-0.231-00.4807-0.0554-0.01080.3583-0.03330.40281.134244.2688-5.718
20.3318-0.07820.11340.0463-0.0650.04820.30260.3240.23460.30850.14790.3255-0.2463-0.75830.00040.78940.07820.06630.6268-0.10460.5772-12.48743.6079-3.0799
30.6829-0.12180.89320.8953-0.07310.6670.2335-0.1013-0.01040.6469-0.20390.1826-0.16750.1752-00.5414-0.0510.03060.33920.04650.42851.321720.73946.6599
40.70650.1360.0650.01630.0470.40070.1082-0.0472-0.2066-0.20020.1810.2510.2485-0.1594-0.00010.5324-0.0195-0.04630.4071-0.00680.4235-15.99950.726913.4203
51.36590.5413-0.4360.2895-0.24460.24770.0279-0.4916-0.8066-0.1856-0.1105-0.463-0.51430.361-0.05420.64060.06260.03380.4613-0.07850.3781-4.810344.608418.9173
60.16940.2481-0.31970.1961-0.14070.71950.1490.0589-0.09510.2027-0.02930.1026-0.00650.2438-0.00010.57430.05930.05740.51990.08380.3725-17.600436.868638.931
70.42930.2846-0.01370.5969-0.08690.2735-0.5050.09360.9311-0.13930.55840.09420.15250.0435-0.00150.3581-0.0255-0.06480.56260.04910.552-24.016355.988532.8997
80.31340.078-0.10290.1837-0.32230.5803-0.4756-0.8677-0.4979-0.8517-0.1139-0.29280.55341.066-0.07580.3550.0563-0.02290.69330.16460.5934-5.003953.110227.2071
91.0908-0.487-0.14290.4986-0.04620.0849-1.1556-0.9469-0.27380.46690.4495-0.1389-0.46060.4934-0.080.56080.0522-0.09340.737-0.08960.4491-3.652756.560334.1054
100.1695-0.00030.18960.30850.04110.1876-0.2022-0.10130.4895-0.39430.36290.48320.1734-0.41690.00030.3623-0.0289-0.01510.58990.00390.4975-23.329951.951530.1016
110.28510.24130.09420.17280.0550.1642-0.8241.1802-0.5333-0.439-0.2208-0.68880.00080.9909-0.00860.5004-0.01660.06940.8240.140.682112.773626.213-14.3467
120.01090.0667-0.0420.76580.43420.5211-0.47840.8754-0.77150.58470.30560.98410.0384-0.2553-0.09210.2025-0.0386-0.00690.5513-0.0150.5776-6.620828.3019-7.9822
130.2565-0.2957-0.29020.7937-0.05050.539-0.34360.2038-0.54170.12180.0591-0.30580.33760.01990.00060.4154-0.01490.04330.3619-0.06220.5037-6.140327.1365-11.3535
140.1921-0.0694-0.07870.1542-0.00860.05060.0838-0.3157-0.00350.35160.2563-1.5128-0.08820.2897-0.00130.3481-0.034-0.07190.5220.11550.739313.179723.9976-6.4222
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 523:561)A523 - 561
2X-RAY DIFFRACTION2(chain A and resid 562:577)A562 - 577
3X-RAY DIFFRACTION3(chain A and resid 578:643)A578 - 643
4X-RAY DIFFRACTION4(chain B and resid 522:562)B522 - 562
5X-RAY DIFFRACTION5(chain B and resid 563:601)B563 - 601
6X-RAY DIFFRACTION6(chain B and resid 602:643)B602 - 643
7X-RAY DIFFRACTION7(chain C and resid 1:7)C1 - 7
8X-RAY DIFFRACTION8(chain C and resid 8:12)C8 - 12
9X-RAY DIFFRACTION9(chain D and resid 1:6)D1 - 6
10X-RAY DIFFRACTION10(chain D and resid 7:13)D7 - 13
11X-RAY DIFFRACTION11(chain H and resid 1:5)H1 - 5
12X-RAY DIFFRACTION12(chain H and resid 6:12)H6 - 12
13X-RAY DIFFRACTION13(chain I and resid 1:9)I1 - 9
14X-RAY DIFFRACTION14(chain I and resid 10:13)I10 - 13

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