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- PDB-3u60: Structure of T4 Bacteriophage Clamp Loader Bound To Open Clamp, D... -

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Basic information

Entry
Database: PDB / ID: 3u60
TitleStructure of T4 Bacteriophage Clamp Loader Bound To Open Clamp, DNA and ATP Analog
Components
  • (DNA polymerase accessory protein ...) x 2
  • DNA polymerase processivity component
  • Primer DNA strand
  • Template DNA strand
KeywordsDNA BINDING PROTEIN/DNA / AAA+ / ATP hydrolase / sliding clamp / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Rad17 RFC-like complex / DNA clamp loader activity / DNA replication factor C complex / Elg1 RFC-like complex / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA polymerase processivity factor activity / viral transcription / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA-templated DNA replication ...Rad17 RFC-like complex / DNA clamp loader activity / DNA replication factor C complex / Elg1 RFC-like complex / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA polymerase processivity factor activity / viral transcription / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA-templated DNA replication / DNA replication / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Bacteriophage clamp loader A subunit, A domain / Bacteriophage clamp loader A subunit, A' domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1260 / Sliding-clamp-loader small subunit gp62 / Sliding-clamp-loader large subunit / : / : / Bacteriophage clamp loader A subunit / Sliding-clamp-loader large subunit, AAA+ ATPase lid domain / Sliding-clamp-loader large subunit, C-terminal domain ...Bacteriophage clamp loader A subunit, A domain / Bacteriophage clamp loader A subunit, A' domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1260 / Sliding-clamp-loader small subunit gp62 / Sliding-clamp-loader large subunit / : / : / Bacteriophage clamp loader A subunit / Sliding-clamp-loader large subunit, AAA+ ATPase lid domain / Sliding-clamp-loader large subunit, C-terminal domain / Sliding clamp, C-terminal / Sliding clamp / gp45 sliding clamp, C terminal / DNA polymerase processivity factor / DNA polymerase processivity factor / Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / : / Helicase, Ruva Protein; domain 3 - #60 / : / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helicase, Ruva Protein; domain 3 / Helix non-globular / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Special / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-08T / ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / Sliding clamp / Sliding-clamp-loader large subunit / Sliding-clamp-loader small subunit
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.34 Å
AuthorsKelch, B.A. / Makino, D.L. / O'Donnell, M. / Kuriyan, J.
CitationJournal: Science / Year: 2011
Title: How a DNA polymerase clamp loader opens a sliding clamp.
Authors: Kelch, B.A. / Makino, D.L. / O'Donnell, M. / Kuriyan, J.
History
DepositionOct 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA polymerase accessory protein 44
C: DNA polymerase accessory protein 44
D: DNA polymerase accessory protein 44
E: DNA polymerase accessory protein 44
I: Template DNA strand
J: Primer DNA strand
A: DNA polymerase accessory protein 62
G: DNA polymerase processivity component
H: DNA polymerase processivity component
F: DNA polymerase processivity component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,94518
Polymers257,94410
Non-polymers2,0018
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34600 Å2
ΔGint-179 kcal/mol
Surface area92610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.518, 118.443, 133.078
Angle α, β, γ (deg.)90.00, 102.06, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42
13
23
33
43

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and resi 1:158
211chain B and resi 1:158
311chain C and resi 1:158
411chain D and resi 17:158
112chain A and resi 159:230
212chain B and resi 159:230
312chain C and resi 159:230
412chain D and resi 159:230
113chain A and resi 234:316
213chain B and resi 234:316
313chain C and resi 234:316
413chain D and resi 234:316

NCS ensembles :
ID
1
2
3

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Components

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DNA polymerase accessory protein ... , 2 types, 5 molecules BCDEA

#1: Protein
DNA polymerase accessory protein 44 / Clamp loader large subunit / Protein Gp44


Mass: 36189.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 44, gp44 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: P04526
#4: Protein DNA polymerase accessory protein 62 / Clamp loader small subunit / Protein Gp62


Mass: 22388.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 62, gp62 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: P04527

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DNA chain , 2 types, 2 molecules IJ

#2: DNA chain Template DNA strand


Mass: 9172.891 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain Primer DNA strand


Mass: 6136.008 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 3 molecules GHF

#5: Protein DNA polymerase processivity component / DNA polymerase accessory protein 45 / Gp45


Mass: 25162.592 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 45, gp45 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: P04525

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Non-polymers , 3 types, 8 molecules

#6: Chemical ChemComp-08T / [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium


Mass: 492.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14BeF3N5O10P2
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5
Details: 20% PEG4k, 0.1M Tris pH7.5, 10mM MgCl2, 20mM NaCl, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2008
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.34→50 Å / Num. all: 40864 / Num. obs: 40789 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Rsym value: 0.201 / Net I/σ(I): 9
Reflection shellResolution: 3.34→3.49 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 5063 / Rsym value: 0.563 / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.34→49.709 Å / SU ML: 0.97 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2817 1553 4 %random
Rwork0.2445 ---
all0.246 38782 --
obs0.246 38782 93.81 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 13.627 Å2 / ksol: 0.292 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.8151 Å20 Å28.4436 Å2
2---16.1653 Å20 Å2
3---5.3502 Å2
Refinement stepCycle: LAST / Resolution: 3.34→49.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16674 897 124 0 17695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01218099
X-RAY DIFFRACTIONf_angle_d1.86924661
X-RAY DIFFRACTIONf_dihedral_angle_d18.8186815
X-RAY DIFFRACTIONf_chiral_restr0.1042815
X-RAY DIFFRACTIONf_plane_restr0.0082988
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1225X-RAY DIFFRACTIONPOSITIONAL
12B1225X-RAY DIFFRACTIONPOSITIONAL0.707
13C1225X-RAY DIFFRACTIONPOSITIONAL0.691
14D1084X-RAY DIFFRACTIONPOSITIONAL0.756
21A560X-RAY DIFFRACTIONPOSITIONAL
22B560X-RAY DIFFRACTIONPOSITIONAL0.31
23C560X-RAY DIFFRACTIONPOSITIONAL0.186
24D491X-RAY DIFFRACTIONPOSITIONAL0.516
31A668X-RAY DIFFRACTIONPOSITIONAL
32B668X-RAY DIFFRACTIONPOSITIONAL0.397
33C668X-RAY DIFFRACTIONPOSITIONAL0.328
34D668X-RAY DIFFRACTIONPOSITIONAL0.492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.34-3.44780.31041240.32693014X-RAY DIFFRACTION84
3.4478-3.5710.34041310.30423164X-RAY DIFFRACTION88
3.571-3.7140.31761350.29233296X-RAY DIFFRACTION91
3.714-3.88290.31331360.2733299X-RAY DIFFRACTION92
3.8829-4.08760.27731420.26073389X-RAY DIFFRACTION94
4.0876-4.34350.29271420.23193379X-RAY DIFFRACTION94
4.3435-4.67870.25521480.21283502X-RAY DIFFRACTION97
4.6787-5.1490.25021460.20853493X-RAY DIFFRACTION97
5.149-5.89310.32441470.25683488X-RAY DIFFRACTION97
5.8931-7.42070.28791500.24583547X-RAY DIFFRACTION98
7.4207-49.71490.23041520.1983658X-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)
13.1142-0.0199-0.8032.0563-0.3546.2866-0.1463-0.01880.37480.58270.35970.4812-0.0319-0.6090.10730.14210.04630.0690.30710.10120.5151-7.0961-1.209220.8668
21.90032.77440.26592.2273-1.14573.756-0.22040.147-0.0444-0.29470.1766-0.0411-0.0064-0.138500.46330.06130.01170.50480.00240.5933-0.2361-4.9395-5.9815
34.5753-0.4917-1.34054.32391.58972.0804-0.04830.12930.3273-0.4489-0.05830.088-0.6784-0.017200.5288-0.01250.0420.3510.08530.431116.1333-34.1341-3.2113
44.0917-0.8327-1.14131.46580.20221.7143-0.01570.08890.6335-0.020.0687-0.0482-0.15510.04820.00080.3532-0.0232-0.02910.37960.05010.462621.2205-2.82479.138
54.15170.743-1.2230.82130.41721.87530.50310.3411-0.54-0.0668-0.3082-0.30450.18740.04280.00060.5810.0389-0.03490.3251-0.01570.434440.5108-17.1736-5.3575
63.4251-0.69830.81484.27660.31755.0560.34070.36830.2065-0.41450.1034-0.27870.05180.38830.00060.27670.05450.13890.34920.00020.459234.2931-48.339-4.0775
73.4837-2.77220.08053.3868-0.83443.53750.0887-0.09790.31380.1196-0.0555-0.4699-0.13070.29060.0040.2338-0.1118-0.09050.3999-0.09950.366743.2084-21.068520.142
83.9211-1.23920.22961.93810.14973.1465-0.2382-0.5091-0.7847-0.2412-0.0824-0.52771.21020.492-0.00940.69920.06090.13870.52410.00290.815956.5477-45.272920.2679
94.29691.30940.41033.30570.54733.7235-0.0309-0.0641-0.24380.11560.274-0.14190.2640.3310.00020.36920.0812-0.02370.37060.06510.329930.4852-62.377913.9364
101.18491.5938-0.74165.3133-2.01086.35370.066-0.2509-0.10380.4668-0.0672-0.19820.81750.212-0.01170.58150.123-0.13750.47530.00560.346737.9737-43.969239.5214
112.1626-0.54730.85971.7746-1.1772.96430.0948-0.5883-1.34130.6950.01280.2588-0.1716-0.3169-0.03321.24850.05380.01560.71460.20820.693830.7079-67.955947.2735
124.0076-0.0048-0.93372.9189-0.7813.71580.1042-0.1395-0.02420.60110.02130.06220.2020.044300.46460.01570.03970.48140.01540.429911.4321-55.819925.0046
130.80911.09380.00651.7029-0.92461.27060.46350.0030.0804-0.1072-0.25530.95090.1059-0.35530.00010.96060.09170.22040.8975-0.01190.8093-11.1355-5.587744.6692
142.37870.1259-0.73781.0713-1.29952.08290.2057-0.00030.76480.3430.03310.605-0.3543-0.55420.00990.42460.0005-0.03270.5512-0.04870.59780.4093-36.444315.5127
153.04292.08060.35651.1591-0.16012.6156-0.0781-0.43070.31420.17290.01030.8304-0.0473-0.6560.00090.92770.13310.02680.8757-0.09090.530412.8102-43.526750.5923
162.2083-0.4143-0.43964.5557-1.58791.3919-0.1571-0.04460.46550.31280.2127-0.5775-0.29910.3938-0.00440.9147-0.1506-0.11830.641-0.22750.926339.17929.049634.6179
174.7552-1.1031-1.13032.47920.58762.5786-0.0184-0.17810.85390.32330.184-0.3892-0.6046-0.086300.88590.02740.01070.4804-0.06710.913114.376723.792827.2725
182.32451.7045-0.85512.6093-0.59211.6756-0.2075-1.1725-0.35250.6730.10780.97620.961-0.027-0.00011.53440.03290.04051.3609-0.05490.911723.57-27.571465.7306
192.54210.2071.95214.468-1.22753.6673-0.1352-0.46360.12140.1382-0.14620.1212-0.20820.0056-00.8653-0.0421-0.10841.015-0.13190.701847.0594-15.053751.9573
202.4914-0.6082-0.02741.2214-0.35672.2283-0.0228-0.96450.61780.1851-0.24330.6292-0.0467-0.089101.12240.09220.16660.9617-0.27181.1964-7.376718.932448.5644
210.95490.09371.28512.091-1.38331.9215-0.3314-0.0591-0.40771.35670.4043-0.01190.13730.262602.11530.15980.261.776-0.05971.2197-11.381.752372.4821
227.1983-3.528-3.32242.0645-0.67613.15430.6683-1.8431.27960.81250.466-1.3655-0.72830.2150.15980.8601-0.0622-0.03910.8698-0.29940.585516.6605-9.154840.9
230.9042-0.7751-0.11931.04360.34560.481-0.6675-0.45320.33020.58440.30551.92470.1457-1.1914-0.48940.54820.12150.02910.9714-0.1391.1927-6.2179-34.968426.7042
244.76030.5929-0.20021.7423-1.37312.35610.2469-1.24010.90121.3198-0.164-0.3484-0.32250.1051-0.01751.12520.0369-0.06040.9188-0.22360.970915.4741-9.362740.3456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain B and resseq 1:159
2X-RAY DIFFRACTION2chain B and resseq 160:232
3X-RAY DIFFRACTION3chain B and resseq 233:319
4X-RAY DIFFRACTION4chain C and resseq 1:159
5X-RAY DIFFRACTION5chain C and resseq 160:232
6X-RAY DIFFRACTION6chain C and resseq 233:319
7X-RAY DIFFRACTION7chain D and resseq 1:159
8X-RAY DIFFRACTION8chain D and resseq 160:232
9X-RAY DIFFRACTION9chain D and resseq 233:319
10X-RAY DIFFRACTION10chain E and resseq 2:159
11X-RAY DIFFRACTION11chain E and resseq 160:220
12X-RAY DIFFRACTION12chain E and resseq 234:319
13X-RAY DIFFRACTION13chain A and resseq 2:37
14X-RAY DIFFRACTION14chain A and resseq 38:113
15X-RAY DIFFRACTION15chain A and resseq 114:187
16X-RAY DIFFRACTION16chain G and resseq 5001:5106
17X-RAY DIFFRACTION17chain G and resseq 5107:5228
18X-RAY DIFFRACTION18chain H and resseq 6001:6106
19X-RAY DIFFRACTION19chain H and resseq 6107:6228
20X-RAY DIFFRACTION20chain F and resseq 7001:7106
21X-RAY DIFFRACTION21chain F and resseq 7107:7228
22X-RAY DIFFRACTION22chain I and resseq 11:30
23X-RAY DIFFRACTION23chain I and resseq 7:10
24X-RAY DIFFRACTION24chain J and resseq 1:20

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