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- PDB-6tun: Helicase domain complex -

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Basic information

Entry
Database: PDB / ID: 6tun
TitleHelicase domain complex
Components
  • CDK-activating kinase assembly factor MAT1
  • General transcription and DNA repair factor IIH helicase subunit XPD
KeywordsNUCLEAR PROTEIN / Helicase / DNA-repair / Transcription / Cell Cylcle
Function / homology
Function and homology information


MMXD complex / Cytosolic iron-sulfur cluster assembly / positive regulation of mitotic recombination / hair cell differentiation / transcription factor TFIIK complex / CAK-ERCC2 complex / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / DNA 5'-3' helicase ...MMXD complex / Cytosolic iron-sulfur cluster assembly / positive regulation of mitotic recombination / hair cell differentiation / transcription factor TFIIK complex / CAK-ERCC2 complex / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / DNA 5'-3' helicase / RNA Polymerase I Transcription Termination / transcription factor TFIID complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / regulation of mitotic cell cycle phase transition / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase I Transcription Initiation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Cyclin E associated events during G1/S transition / Formation of HIV elongation complex in the absence of HIV Tat / Cyclin A:Cdk2-associated events at S phase entry / Cyclin A/B1/B2 associated events during G2/M transition / cyclin-dependent protein kinase holoenzyme complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / regulation of G1/S transition of mitotic cell cycle / RNA Polymerase II Pre-transcription Events / positive regulation of smooth muscle cell proliferation / transcription-coupled nucleotide-excision repair / DNA helicase activity / chromosome segregation / G1/S transition of mitotic cell cycle / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / NoRC negatively regulates rRNA expression / transcription by RNA polymerase II / spindle / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Cyclin D associated events in G1 / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / 4 iron, 4 sulfur cluster binding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / response to oxidative stress / 5'-3' DNA helicase activity / damaged DNA binding / protein-macromolecule adaptor activity / apoptotic process / DNA repair / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / ATP hydrolysis activity / nucleoplasm / zinc ion binding / metal ion binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / MAT1 C-terminal CAK anchor / RAD3/XPD family / Helical and beta-bridge domain / Helical and beta-bridge domain / ATP-dependent helicase Rad3/Chl1-like / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) ...: / MAT1 C-terminal CAK anchor / RAD3/XPD family / Helical and beta-bridge domain / Helical and beta-bridge domain / ATP-dependent helicase Rad3/Chl1-like / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / HELICc2 / ATP-dependent helicase, C-terminal / Helicase C-terminal domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
General transcription and DNA repair factor IIH helicase subunit XPD / CDK-activating kinase assembly factor MAT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.07 Å
AuthorsSauer, F. / Kisker, C.
CitationJournal: Nat Commun / Year: 2020
Title: In TFIIH the Arch domain of XPD is mechanistically essential for transcription and DNA repair.
Authors: Peissert, S. / Sauer, F. / Grabarczyk, D.B. / Braun, C. / Sander, G. / Poterszman, A. / Egly, J.M. / Kuper, J. / Kisker, C.
History
DepositionJan 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: General transcription and DNA repair factor IIH helicase subunit XPD
B: General transcription and DNA repair factor IIH helicase subunit XPD
D: CDK-activating kinase assembly factor MAT1
C: CDK-activating kinase assembly factor MAT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7626
Polymers63,6914
Non-polymers712
Water2,720151
1
A: General transcription and DNA repair factor IIH helicase subunit XPD
D: CDK-activating kinase assembly factor MAT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8813
Polymers31,8462
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: General transcription and DNA repair factor IIH helicase subunit XPD
C: CDK-activating kinase assembly factor MAT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8813
Polymers31,8462
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.940, 78.350, 92.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein General transcription and DNA repair factor IIH helicase subunit XPD / TFIIH subunit XPD / Basic transcription factor 2 80 kDa subunit / BTF2 p80 / CXPD / DNA excision ...TFIIH subunit XPD / Basic transcription factor 2 80 kDa subunit / BTF2 p80 / CXPD / DNA excision repair protein ERCC-2 / DNA repair protein complementing XP-D cells / TFIIH basal transcription factor complex 80 kDa subunit / TFIIH p80 / Xeroderma pigmentosum group D-complementing protein


Mass: 22539.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Arch domain / Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC2, XPD, XPDC / Production host: Escherichia coli (E. coli) / References: UniProt: P18074, DNA helicase
#2: Protein CDK-activating kinase assembly factor MAT1 / CDK7/cyclin-H assembly factor / Cyclin-G1-interacting protein / Menage a trois / RING finger ...CDK7/cyclin-H assembly factor / Cyclin-G1-interacting protein / Menage a trois / RING finger protein 66 / RING finger protein MAT1 / p35 / p36


Mass: 9305.615 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MNAT1, CAP35, MAT1, RNF66 / Production host: Escherichia coli (E. coli) / References: UniProt: P51948
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris pH 8.5 25% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0064 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0064 Å / Relative weight: 1
ReflectionResolution: 2.07→46.71 Å / Num. obs: 33675 / % possible obs: 99.6 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rpim(I) all: 0.038 / Net I/σ(I): 11.6
Reflection shellResolution: 2.07→2.13 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 2591 / CC1/2: 0.759 / Rpim(I) all: 0.439

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: SAD / Resolution: 2.07→46.71 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.63
RfactorNum. reflection% reflection
Rfree0.2273 1286 3.83 %
Rwork0.192 --
obs0.1933 33596 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.07→46.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3863 0 2 151 4016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074047
X-RAY DIFFRACTIONf_angle_d0.8885479
X-RAY DIFFRACTIONf_dihedral_angle_d17.8122522
X-RAY DIFFRACTIONf_chiral_restr0.047624
X-RAY DIFFRACTIONf_plane_restr0.005718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.15290.30881420.29223508X-RAY DIFFRACTION99
2.1529-2.25090.30431360.25033544X-RAY DIFFRACTION99
2.2509-2.36950.26661460.23323555X-RAY DIFFRACTION100
2.3695-2.5180.27541420.21933542X-RAY DIFFRACTION99
2.518-2.71240.23861400.2053571X-RAY DIFFRACTION99
2.7124-2.98530.2631450.20813569X-RAY DIFFRACTION100
2.9853-3.41720.25691490.19283596X-RAY DIFFRACTION99
3.4172-4.30480.18061190.16773648X-RAY DIFFRACTION99
4.3048-46.710.19931670.17113777X-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)
14.39672.7012-3.21118.5406-2.83186.68590.32080.09220.1130.80740.2740.4102-0.9106-0.2278-0.57050.43340.13880.04080.39840.03750.4974-23.091-9.694633.9899
29.20440.8132-2.15372.43870.21352.8593-0.51580.29930.0925-0.23980.52130.8181-0.0063-0.73130.12090.503-0.00940.08090.43360.01310.6843-30.6231-28.721538.6664
34.9407-1.08691.40312.4003-3.50566.1820.38980.4216-1.0254-1.254-0.0520.36850.9727-0.4082-0.10490.6619-0.004-0.08250.3311-0.03730.5085-21.6116-30.547830.8528
48.72934.1858-4.31775.1372-2.69646.07050.2358-0.08520.56690.41810.19240.4971-0.3745-0.0314-0.43340.36080.01730.06150.2687-0.0180.328-13.5578-14.172535.1888
56.8558-2.0681-3.6653.18042.76043.4035-0.4082-0.5310.61270.24180.7438-0.73580.05310.949-0.3740.6885-0.1674-0.02190.484-0.0080.4297-2.7044-3.71324.3418
63.79351.5309-3.71726.099-1.85113.66150.1866-0.0469-0.24790.1471-0.0659-0.3708-0.42470.1114-0.07710.4450.02750.02740.3440.00730.3259-4.5424-17.502430.1173
76.55070.6149-3.51967.52220.52536.21280.09690.60820.0087-0.1191-0.08521.0184-0.2311-0.59760.07890.4263-0.0084-0.00670.30410.01570.4186-23.8317-21.113328.8631
84.9631-4.2076-4.42125.33164.64587.46410.2414-0.0754-0.3464-0.3805-0.0780.5009-0.62930.017-0.01380.3395-0.0063-0.02520.27980.00870.3916-15.5634-18.642919.5898
90.3496-1.2654-1.94556.41283.50697.1959-0.2868-0.2448-0.45941.0820.9637-0.18441.19060.7201-0.72910.6340.1341-0.17880.4646-0.02220.4857-10.2624-39.34214.3018
108.0106-0.7649-1.94433.36342.62763.23070.2751-1.3441-0.74390.1852-0.04231.296-1.1308-0.5116-0.12070.8466-0.0672-0.1360.69950.10370.5345-16.0484-29.97715.5792
116.7005-5.08574.27953.7246-2.91744.35250.2238-0.0927-0.1436-0.30720.0040.09180.51490.1651-0.45470.4701-0.0594-0.12480.33250.01080.4322-23.7228-29.1867-14.305
127.8888-0.43824.1965.50731.97293.5456-0.30050.11070.4181-0.2110.06560.3885-0.4586-0.17930.15520.4325-0.004-0.13170.34820.00490.5147-30.0174-10.4119-15.0789
131.6092-1.00270.58125.7787-0.85020.6827-0.5633-0.35840.9332-0.375-0.3370.3123-1.4129-0.19590.68350.63070.0388-0.08680.418-0.0690.4856-19.2241-8.6722-8.2439
146.3444-1.70842.70124.016-1.65256.20520.17720.6848-0.4745-0.72560.0512-0.1621-0.0630.4115-0.31620.4144-0.0291-0.03570.4-0.08280.4498-12.3436-25.5836-10.5717
154.78064.65812.79364.63793.21533.3967-0.29480.6929-0.8688-0.75050.1432-0.9301-0.19491.2233-0.51430.70490.1373-0.29230.5702-0.20970.8106-1.354-35.15640.724
165.2777-0.75373.17697.43-3.94234.0482-0.25870.3472-0.2117-0.36060.0805-0.9299-0.59850.8560.12950.3411-0.03110.05070.4896-0.14220.4331-3.9234-21.0396-5.5386
172.81731.45082.81494.62611.91647.4296-0.2439-0.7560.18540.08090.14890.5711-0.3244-0.23350.13010.4325-0.025-0.04230.29790.00810.4373-20.0126-16.6677-3.9545
187.8154-6.71225.7396.1075-5.83867.3287-0.5325-1.0164-0.55220.11150.88382.3911-0.1985-2.7585-0.60970.74050.0777-0.32360.7349-0.08410.8178-32.3568-27.3667-8.1223
199.14014.6344.72265.47215.88967.02230.2594-0.5811-0.15080.4418-0.1873-0.01270.3177-0.1837-0.07940.33780.0079-0.05170.3225-0.00160.3417-17.1462-24.30560.3738
205.31944.23434.46153.62844.00024.28110.32850.50270.2613-0.00770.08880.3715-0.49120.307-0.51810.48930.0239-0.02210.3483-0.0220.3171-7.3595-11.476814.4064
210.90081.74712.63663.42754.48276.8092-0.46150.27020.4535-1.09250.09241.4655-1.63850.37390.32060.8176-0.10090.03920.4676-0.01610.5811-10.80220.039419.8965
229.1852-3.35021.41953.1234-2.77313.4984-0.2505-0.82950.40620.97530.4592-0.3379-0.60190.3081-0.32290.5677-0.01750.01360.5178-0.0280.3116-6.7016-18.815944.7486
232.75692.7790.0455.41163.26527.4536-0.0671-0.2064-0.36360.16710.2797-0.41150.07950.2957-0.12690.46440.04910.02570.31450.0230.3542-10.9945-31.959739.6877
244.4519-0.0136-2.81097.44182.22282.6735-0.1781-1.6048-1.06791.3004-0.0239-0.40710.90990.99680.10431.02110.2619-0.00690.84780.17210.6574-7.9498-31.600552.8598
254.3557-0.53162.32723.34292.05383.29110.19831.1113-0.8449-0.5490.6048-0.90171.13670.8399-0.90510.84410.01890.07950.7315-0.07370.5688-5.7641-20.7904-20.4117
264.6315-1.80760.16739.3553.20577.0848-0.18360.28280.1045-0.85590.165-0.1369-0.5332-0.15880.00550.5798-0.1085-0.02840.39950.04470.3361-9.924-7.4111-15.615
271.4975-2.8546-0.50955.72821.28990.38320.63981.40130.5399-3.0631-1.1155-1.6367-1.5680.5110.95951.8867-0.27660.33141.1150.26810.8639-7.6331-8.3712-29.044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 246 through 276 )
2X-RAY DIFFRACTION2chain 'A' and (resid 277 through 289 )
3X-RAY DIFFRACTION3chain 'A' and (resid 290 through 325 )
4X-RAY DIFFRACTION4chain 'A' and (resid 326 through 343 )
5X-RAY DIFFRACTION5chain 'A' and (resid 344 through 353 )
6X-RAY DIFFRACTION6chain 'A' and (resid 354 through 368 )
7X-RAY DIFFRACTION7chain 'A' and (resid 369 through 391 )
8X-RAY DIFFRACTION8chain 'A' and (resid 392 through 419 )
9X-RAY DIFFRACTION9chain 'A' and (resid 420 through 439 )
10X-RAY DIFFRACTION10chain 'B' and (resid 246 through 252 )
11X-RAY DIFFRACTION11chain 'B' and (resid 253 through 276 )
12X-RAY DIFFRACTION12chain 'B' and (resid 277 through 289 )
13X-RAY DIFFRACTION13chain 'B' and (resid 290 through 325 )
14X-RAY DIFFRACTION14chain 'B' and (resid 326 through 344 )
15X-RAY DIFFRACTION15chain 'B' and (resid 345 through 353 )
16X-RAY DIFFRACTION16chain 'B' and (resid 354 through 368 )
17X-RAY DIFFRACTION17chain 'B' and (resid 369 through 385 )
18X-RAY DIFFRACTION18chain 'B' and (resid 386 through 394 )
19X-RAY DIFFRACTION19chain 'B' and (resid 395 through 409 )
20X-RAY DIFFRACTION20chain 'B' and (resid 410 through 419 )
21X-RAY DIFFRACTION21chain 'B' and (resid 420 through 439 )
22X-RAY DIFFRACTION22chain 'D' and (resid 66 through 81 )
23X-RAY DIFFRACTION23chain 'D' and (resid 82 through 111 )
24X-RAY DIFFRACTION24chain 'D' and (resid 112 through 130 )
25X-RAY DIFFRACTION25chain 'C' and (resid 65 through 81 )
26X-RAY DIFFRACTION26chain 'C' and (resid 82 through 111 )
27X-RAY DIFFRACTION27chain 'C' and (resid 112 through 129 )

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