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- PDB-5uj7: Structure of the active form of human Origin Recognition Complex ... -

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Basic information

Entry
Database: PDB / ID: 5uj7
TitleStructure of the active form of human Origin Recognition Complex ATPase motor module, complex subunitS 1, 4, 5
Components(Origin recognition complex subunit ...) x 3
KeywordsDNA BINDING PROTEIN / Replication / DNA-binding / AAA+ ATPase
Function / homology
Function and homology information


polar body extrusion after meiotic divisions / CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / nuclear origin of replication recognition complex / mitotic DNA replication checkpoint signaling / G1/S-Specific Transcription / DNA replication origin binding / regulation of DNA replication / DNA replication initiation ...polar body extrusion after meiotic divisions / CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / nuclear origin of replication recognition complex / mitotic DNA replication checkpoint signaling / G1/S-Specific Transcription / DNA replication origin binding / regulation of DNA replication / DNA replication initiation / protein polymerization / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / Assembly of the ORC complex at the origin of replication / Assembly of the pre-replicative complex / Orc1 removal from chromatin / DNA replication / chromosome, telomeric region / nucleotide binding / chromatin binding / chromatin / nucleolus / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Cdc6, C-terminal / CDC6, C terminal / CDC6, C terminal winged helix domain / Origin recognition complex subunit 4 / Origin recognition complex, subunit 5 / Origin recognition complex subunit 4, C-terminal / : / : / Origin recognition complex (ORC) subunit 4 C-terminus / Origin recognition complex (ORC) subunit 5 C-terminus ...Cdc6, C-terminal / CDC6, C terminal / CDC6, C terminal winged helix domain / Origin recognition complex subunit 4 / Origin recognition complex, subunit 5 / Origin recognition complex subunit 4, C-terminal / : / : / Origin recognition complex (ORC) subunit 4 C-terminus / Origin recognition complex (ORC) subunit 5 C-terminus / ORC5, lid domain / Orc1-like, AAA ATPase domain / AAA ATPase domain / AAA lid domain / AAA lid domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / Origin recognition complex subunit 5 / Origin recognition complex subunit 4 / Origin recognition complex subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.394 Å
AuthorsTocilj, A. / Elkayam, E. / On, K.F. / Joshua-Tor, L.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2017
Title: Structure of the active form of human origin recognition complex and its ATPase motor module.
Authors: Ante Tocilj / Kin Fan On / Zuanning Yuan / Jingchuan Sun / Elad Elkayam / Huilin Li / Bruce Stillman / Leemor Joshua-Tor /
Abstract: Binding of the Origin Recognition Complex (ORC) to origins of replication marks the first step in the initiation of replication of the genome in all eukaryotic cells. Here, we report the structure of ...Binding of the Origin Recognition Complex (ORC) to origins of replication marks the first step in the initiation of replication of the genome in all eukaryotic cells. Here, we report the structure of the active form of human ORC determined by X-ray crystallography and cryo-electron microscopy. The complex is composed of an ORC1/4/5 motor module lobe in an organization reminiscent of the DNA polymerase clamp loader complexes. A second lobe contains the ORC2/3 subunits. The complex is organized as a double-layered shallow corkscrew, with the AAA+ and AAA+-like domains forming one layer, and the winged-helix domains (WHDs) forming a top layer. CDC6 fits easily between ORC1 and ORC2, completing the ring and the DNA-binding channel, forming an additional ATP hydrolysis site. Analysis of the ATPase activity of the complex provides a basis for understanding ORC activity as well as molecular defects observed in Meier-Gorlin Syndrome mutations.
History
DepositionJan 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_assembly ...pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details ..._pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Origin recognition complex subunit 1
C: Origin recognition complex subunit 4
E: Origin recognition complex subunit 5
B: Origin recognition complex subunit 1
D: Origin recognition complex subunit 4
F: Origin recognition complex subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,73818
Polymers255,5206
Non-polymers3,21912
Water0
1
A: Origin recognition complex subunit 1
C: Origin recognition complex subunit 4
E: Origin recognition complex subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,3699
Polymers127,7603
Non-polymers1,6096
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14340 Å2
ΔGint-53 kcal/mol
Surface area42640 Å2
MethodPISA
2
B: Origin recognition complex subunit 1
D: Origin recognition complex subunit 4
F: Origin recognition complex subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,3699
Polymers127,7603
Non-polymers1,6096
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14120 Å2
ΔGint-62 kcal/mol
Surface area43460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.887, 81.141, 151.947
Angle α, β, γ (deg.)90.00, 97.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Origin recognition complex subunit ... , 3 types, 6 molecules ABCDEF

#1: Protein Origin recognition complex subunit 1 / / Replication control protein 1


Mass: 44179.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ORC1, ORC1L, PARC1
Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
References: UniProt: Q13415
#2: Protein Origin recognition complex subunit 4 /


Mass: 50443.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ORC4, ORC4L
Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
References: UniProt: O43929
#3: Protein Origin recognition complex subunit 5 /


Mass: 33137.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ORC5, ORC5L
Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
References: UniProt: O43913

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Non-polymers , 3 types, 12 molecules

#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K

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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: 2.96 Å3/Da / Density % sol: 58.48 % / Description: Thin plates 100X100 microns
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 22% Ethylene glycol 8% Propylene glycol 10mg/ml protein 1:1 ratio

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.39→20 Å / Num. obs: 39700 / % possible obs: 97 % / Redundancy: 3.7 % / Biso Wilson estimate: 104 Å2 / Rsym value: 0.14 / Net I/σ(I): 8.75
Reflection shellResolution: 3.39→3.52 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.2 / CC1/2: 0.524 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XGC

4xgc


Resolution: 3.394→19.882 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2811 1963 4.94 %
Rwork0.2421 --
obs0.245 39700 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.394→19.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15678 0 192 0 15870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416177
X-RAY DIFFRACTIONf_angle_d0.71821904
X-RAY DIFFRACTIONf_dihedral_angle_d10.4959800
X-RAY DIFFRACTIONf_chiral_restr0.0432504
X-RAY DIFFRACTIONf_plane_restr0.0042753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3936-3.47810.42081360.38042509X-RAY DIFFRACTION93
3.4781-3.57160.38591440.35422744X-RAY DIFFRACTION100
3.5716-3.6760.38631210.33152156X-RAY DIFFRACTION79
3.676-3.79390.35531320.31462695X-RAY DIFFRACTION99
3.7939-3.92850.33731350.3062749X-RAY DIFFRACTION100
3.9285-4.08450.36261360.28282748X-RAY DIFFRACTION100
4.0845-4.26860.37961370.25692747X-RAY DIFFRACTION100
4.2686-4.49130.29661590.23442732X-RAY DIFFRACTION100
4.4913-4.7690.25641520.22432751X-RAY DIFFRACTION100
4.769-5.13140.31831370.22212742X-RAY DIFFRACTION100
5.1314-5.6370.29811380.23822765X-RAY DIFFRACTION100
5.637-6.42850.3611470.27992770X-RAY DIFFRACTION100
6.4285-8.01010.28051470.23762792X-RAY DIFFRACTION100
8.0101-19.88230.21631420.16412837X-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)
11.2974-0.74070.90560.5668-0.69080.86940.68060.9099-0.94120.5657-0.60711.40661.58010.6776-0.05661.00910.1013-0.33131.1938-0.15821.479289.5395-13.4036-64.6398
21.0282-0.9614-0.18932.4765-0.91522.63460.22990.1522-0.2909-0.01370.02290.08420.46970.126-01.214-0.0839-0.02591.0127-0.09390.720371.9223.8042-81.4605
31.0237-0.2101-0.44560.39050.61830.99040.2036-0.12810.18270.01580.0088-0.32640.7575-0.04260.00011.2680.0741-0.21590.8570.01870.982282.1343-12.7601-58.2678
40.57060.1040.39150.89910.51940.19881.2199-0.7884-1.4518-1.9513-0.70591.33460.38990.63570.42541.29130.1641-0.14551.06090.21541.299786.0956-3.072-42.3019
53.120.32570.36062.42831.01391.4621-0.17930.1224-0.16171.2956-0.12440.56630.02730.0798-0.00021.0091-0.21720.08010.91470.09740.494875.927318.6066-30.7279
61.7074-0.04471.10040.0753-0.29790.775-0.183-0.12320.23140.34450.2164-0.30930.4342-0.08990.00070.95130.1628-0.05431.13860.0321.4022106.144812.3301-43.4808
72.5545-0.22490.9053.4075-0.32451.74750.39260.1453-0.3515-0.38260.0302-0.4798-0.01720.3374-0.00010.79770.06630.10680.95070.02380.803695.19612.4287-62.3852
80.65140.18730.29031.0104-0.78011.028-0.7263-0.0838-0.6190.6963-0.04211.08910.6222-0.04130.00030.88310.0849-0.11690.90970.03480.990186.6128.4748-55.574
90.0187-0.1842-0.35391.4891-0.65331.79180.3592-0.1071-0.37210.1965-0.0422-0.01170.93410.25820.00040.91570.07550.04911.01820.19211.21996.66078.8569-40.7446
10-0.13670.02680.08772.0070.89011.33310.01740.17980.03230.8507-0.2363-0.65440.14620.1924-0.00261.1468-0.2157-0.4180.89880.21220.830496.82628.4864-25.4529
110.6878-0.14970.66630.79410.58341.1580.4467-0.20621.2634-1.2421-1.16060.8254-0.583-0.3379-0.10261.04610.08260.30780.9988-0.07080.879468.089351.8355-27.3003
122.097-0.2819-0.50910.40960.78571.47731.3131-0.23030.14040.9476-0.7042-0.14751.2463-0.47760.08141.0545-0.26730.17240.82550.02260.521474.340742.7637-24.732
130.3874-0.00250.47270.39150.52470.95740.5785-0.5689-0.9706-0.0394-0.4729-0.1311-0.25220.2801-00.8997-0.0619-0.1670.89110.03110.9615102.175339.7715-35.8481
141.45890.132-1.05411.1748-1.09051.4752-0.0841-0.3988-0.0194-0.82440.19650.3216-0.66690.1058-0.00120.7962-0.05690.09231.17080.05530.804798.255640.6964-53.7858
153.44791.4336-1.35425.62721.37622.07860.4942-0.6959-0.8815-0.83120.495-2.5407-0.4445-0.242-0.44050.6067-0.15970.12211.12410.1637-0.507399.044837.3377-50.4349
162.27991.36690.05740.8691-0.20772.3920.1170.2656-0.05320.5411-0.4763-0.59430.223-0.040300.8009-0.0466-0.11850.79630.2350.979493.058732.93-42.1869
173.06651.486-0.63332.7221-0.40.2930.3452-0.0348-1.7341-0.982-0.3648-1.7857-0.4658-0.48570.00891.6041-0.07110.03731.06930.0670.446793.575763.081-27.0977
180.3451-0.190.42831.6250.22350.9315-0.5016-0.35861.6881-1.25560.06133.2658-2.5017-0.24150.02191.6149-0.1822-0.11541.0437-0.15361.435387.364173.8675-23.6778
191.87630.7314-0.48480.38250.2151.348-0.2271-0.09440.1752-0.93650.53011.7854-0.54990.23730.09770.7076-0.0852-0.24690.99520.38441.5294148.827125.5528-30.5764
202.15810.8720.13472.8605-1.15590.388-0.05850.2063-0.3449-0.01060.34440.42340.1610.001800.7380.0064-0.08670.97670.09711.2515151.019120.0232-25.8977
21-0.03160.1828-0.17510.3664-0.26370.13380.5040.20360.64390.2869-0.01170.4818-1.3664-0.60720.00141.25290.15420.13181.0868-0.07841.1156168.67948.8658-24.5352
226.9933-1.08971.78980.1436-0.31641.12660.16191.08932.62083.0611-0.2243-0.0991-1.81990.2402-0.47062.3474-0.11650.82720.4249-0.19891.9308172.565159.9846-18.154
230.9988-0.022-0.64750.4024-0.71721.0961-1.06551.0452-1.9298-0.61750.6786-0.6768-0.2594-0.05920.00051.857-0.3497-0.20831.228-0.47361.0693152.4424-2.1279-36.934
242.73761.1831.16791.5216-0.51343.2775-0.48690.2520.564-0.02830.06770.26290.0943-0.03440.00010.8014-0.033-0.18211.00640.0551.4141134.6784-2.5927-24.2299
251.7006-0.08970.91770.31590.34580.3482-0.15080.3601-0.593-0.19430.1580.10220.12230.62501.04560.09340.23341.1512-0.1640.9861164.8953.2885-32.8063
261.17180.84490.03252.02840.32932.25660.0511-0.15470.0080.251-0.2867-0.2827-0.43090.4581-00.993-0.11840.07720.95410.02340.6252169.894331.3174-3.8716
270.3071-0.2813-0.18350.46190.1730.0582-0.4050.1656-0.58751.0859-0.4578-0.26371.0997-0.48840.00131.0664-0.12680.17510.9017-0.11671.1973131.4459-27.6024-19.599
281.8885-1.20150.35391.37640.71581.16390.4693-0.10270.10540.0071-0.08240.17590.0241-0.1537-00.7796-0.11580.06021.12640.00911.7062115.2987-18.7498-3.8008
291.2479-1.0905-0.96662.25731.63191.46450.1563-0.1025-0.1621-0.3870.12340.45560.19260.018400.8953-0.0290.14270.96010.03711.7152124.0621-13.2123-5.0089
300.30250.19630.15770.48990.1288-0.0996-0.55520.093-0.3113-0.84870.00791.5522-0.59240.2946-0.02511.69410.31540.28720.99110.06741.3188154.044-17.3697-16.5221
310.86660.90450.15373.1149-1.43361.09850.14780.1016-0.28450.32070.2177-0.60820.12510.34670.00140.6628-0.04040.00671.07890.09450.8052165.73014.4204-6.8737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 490 through 508 )
2X-RAY DIFFRACTION2chain 'A' and (resid 509 through 674 )
3X-RAY DIFFRACTION3chain 'A' and (resid 675 through 734 )
4X-RAY DIFFRACTION4chain 'A' and (resid 735 through 771 )
5X-RAY DIFFRACTION5chain 'A' and (resid 772 through 861 )
6X-RAY DIFFRACTION6chain 'C' and (resid 17 through 55 )
7X-RAY DIFFRACTION7chain 'C' and (resid 56 through 182 )
8X-RAY DIFFRACTION8chain 'C' and (resid 183 through 203 )
9X-RAY DIFFRACTION9chain 'C' and (resid 204 through 244 )
10X-RAY DIFFRACTION10chain 'C' and (resid 245 through 338 )
11X-RAY DIFFRACTION11chain 'C' and (resid 339 through 381 )
12X-RAY DIFFRACTION12chain 'C' and (resid 382 through 432 )
13X-RAY DIFFRACTION13chain 'E' and (resid 8 through 43 )
14X-RAY DIFFRACTION14chain 'E' and (resid 44 through 108 )
15X-RAY DIFFRACTION15chain 'E' and (resid 109 through 134 )
16X-RAY DIFFRACTION16chain 'E' and (resid 135 through 183 )
17X-RAY DIFFRACTION17chain 'E' and (resid 184 through 231 )
18X-RAY DIFFRACTION18chain 'E' and (resid 232 through 268 )
19X-RAY DIFFRACTION19chain 'F' and (resid 10 through 108 )
20X-RAY DIFFRACTION20chain 'F' and (resid 109 through 183 )
21X-RAY DIFFRACTION21chain 'F' and (resid 184 through 231 )
22X-RAY DIFFRACTION22chain 'F' and (resid 232 through 268 )
23X-RAY DIFFRACTION23chain 'D' and (resid 17 through 55 )
24X-RAY DIFFRACTION24chain 'D' and (resid 56 through 203 )
25X-RAY DIFFRACTION25chain 'D' and (resid 204 through 310 )
26X-RAY DIFFRACTION26chain 'D' and (resid 311 through 432 )
27X-RAY DIFFRACTION27chain 'B' and (resid 490 through 508 )
28X-RAY DIFFRACTION28chain 'B' and (resid 509 through 575 )
29X-RAY DIFFRACTION29chain 'B' and (resid 576 through 734 )
30X-RAY DIFFRACTION30chain 'B' and (resid 735 through 771 )
31X-RAY DIFFRACTION31chain 'B' and (resid 772 through 861 )

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