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- PDB-4xgc: Crystal structure of the eukaryotic origin recognition complex -

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Basic information

Entry
Database: PDB / ID: 4xgc
TitleCrystal structure of the eukaryotic origin recognition complex
Components(Origin recognition complex subunit ...) x 7
KeywordsDNA BINDING PROTEIN / protein complex
Function / homology
Function and homology information


alpha-heterochromatin / larval feeding behavior / CDC6 association with the ORC:origin complex / septin cytoskeleton / septin cytoskeleton organization / Activation of ATR in response to replication stress / Activation of the pre-replicative complex / eggshell chorion gene amplification / Orc1 removal from chromatin / DNA amplification ...alpha-heterochromatin / larval feeding behavior / CDC6 association with the ORC:origin complex / septin cytoskeleton / septin cytoskeleton organization / Activation of ATR in response to replication stress / Activation of the pre-replicative complex / eggshell chorion gene amplification / Orc1 removal from chromatin / DNA amplification / positive regulation of border follicle cell migration / origin recognition complex / Assembly of the ORC complex at the origin of replication / nuclear origin of replication recognition complex / olfactory learning / nuclear pre-replicative complex / DNA replication preinitiation complex / mitotic chromosome condensation / mitotic DNA replication checkpoint signaling / chromosome condensation / DNA replication origin binding / DNA replication initiation / nuclear pore / ribonucleoprotein complex binding / heterochromatin / GTPase activator activity / learning / mitotic spindle organization / DNA-templated DNA replication / mitotic cell cycle / learning or memory / DNA replication / chromatin binding / protein homodimerization activity / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding / nucleus / plasma membrane
Similarity search - Function
Origin recognition complex, subunit 6, metazoa/plant / : / ORC6 second cyclin-like domain / Origin recognition complex subunit 3, insertion domain / Origin recognition complex subunit 3 insertion domain / CDC6, C terminal / Origin recognition complex, subunit 6 / Origin recognition complex subunit 6 (ORC6) / Cdc6, C-terminal / CDC6, C terminal winged helix domain ...Origin recognition complex, subunit 6, metazoa/plant / : / ORC6 second cyclin-like domain / Origin recognition complex subunit 3, insertion domain / Origin recognition complex subunit 3 insertion domain / CDC6, C terminal / Origin recognition complex, subunit 6 / Origin recognition complex subunit 6 (ORC6) / Cdc6, C-terminal / CDC6, C terminal winged helix domain / Origin recognition complex subunit 4 / Origin recognition complex, subunit 3 / Origin recognition complex, subunit 5 / Origin recognition complex subunit 4, C-terminal / Origin recognition complex subunit 3, winged helix C-terminal / Origin recognition complex subunit 3, N-terminal / : / : / Origin recognition complex (ORC) subunit 3 N-terminus / Origin recognition complex (ORC) subunit 4 C-terminus / Origin recognition complex (ORC) subunit 5 C-terminus / Origin recognition complex winged helix C-terminal / ORC5, lid domain / Orc1-like, AAA ATPase domain / Origin recognition complex subunit 2 RecA-like domain / AAA ATPase domain / Origin recognition complex, subunit 2 / AAA lid domain / AAA lid domain / : / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / 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
: / Origin recognition complex subunit 1 / Origin recognition complex subunit 2 / Origin recognition complex subunit 5 / Origin recognition complex subunit 3 / Origin recognition complex subunit 4 / Origin recognition complex subunit 6
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å
AuthorsBleichert, F. / Botchan, M.R. / Berger, J.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071747 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA R37-30490 United States
CitationJournal: Nature / Year: 2015
Title: Crystal structure of the eukaryotic origin recognition complex.
Authors: Bleichert, F. / Botchan, M.R. / Berger, J.M.
History
DepositionDec 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Data collection
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Origin recognition complex subunit 2
C: Origin recognition complex subunit 3
E: Origin recognition complex subunit 5
A: Origin recognition complex subunit 1
G: Origin recognition complex subunit 2
F: Origin recognition complex subunit 6
D: Origin recognition complex subunit 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,6349
Polymers277,5597
Non-polymers752
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24310 Å2
ΔGint-127 kcal/mol
Surface area90360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.545, 258.983, 257.001
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
DetailsThe depositor states that the biological assembly is hexameric, not heptameric. Orc2 was deposited as 2 different chains because the N-terminus could only be built as a discontinuous polyalanine model. However, both chains belong to the same polypeptide.

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Components

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Origin recognition complex subunit ... , 7 types, 7 molecules BCEAGFD

#1: Protein Origin recognition complex subunit 2 / DmORC2


Mass: 40106.762 Da / Num. of mol.: 1 / Fragment: residues 266-618
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Orc2, CG3041 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q24168
#2: Protein Origin recognition complex subunit 3 / FI24229p1 / GH28787p / LP02234p1 / Latheo


Mass: 77650.078 Da / Num. of mol.: 1 / Fragment: residues 47-721
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: lat, CG34315-RB, lat-RA, CG4088, Dmel_CG4088 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7K2L1
#3: Protein Origin recognition complex subunit 5


Mass: 52175.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Orc5, CG7833 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q24169
#4: Protein Origin recognition complex subunit 1 / DmORC1


Mass: 43910.801 Da / Num. of mol.: 1 / Fragment: residues 533-924
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Orc1, CG10667 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O16810
#5: Protein/peptide Origin recognition complex subunit 2


Mass: 3507.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Orc2, CG3041 / Production host: Trichoplusia ni (cabbage looper)
#6: Protein Origin recognition complex subunit 6


Mass: 8204.343 Da / Num. of mol.: 1 / Fragment: residues 187-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Orc6, CG1584 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y1B2
#7: Protein Origin recognition complex subunit 4 / LD43280p


Mass: 52004.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Orc4, CG2917, Dmel_CG2917 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9W102, nucleoside-triphosphate phosphatase

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Non-polymers , 2 types, 2 molecules

#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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Details

Has protein modificationN
Sequence detailsTHE AUTHOR STATES THAT CHAIN G IS LIKELY PART OF THE N-TERMINUS OF CHAIN B. 61 N-TERMINAL RESIDUES ...THE AUTHOR STATES THAT CHAIN G IS LIKELY PART OF THE N-TERMINUS OF CHAIN B. 61 N-TERMINAL RESIDUES ARE MISSING (DISORDERED). OWING TO LOW RESOLUTION, IT WAS NOT POSSIBLE TO ACCURATELY ASSIGN THE SIDE CHAINS AND IDENTIFY THE PEPTIDE. THE N-TERMINUS WAS MODELED AS ALA, BUT THE SEQUENCE ALIGNMENT IS UNKNOWN, AND WAS THEREFORE CHANGED TO UNK IN THIS ENTRY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.37 Å3/Da / Density % sol: 71.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: PIPES (pH 7.5), magnesium chloride, ammonium acetate, PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332, 1.71083
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
21.710831
ReflectionResolution: 3.5→48.8 Å / Num. obs: 61418 / % possible obs: 100 % / Redundancy: 8.4 % / Biso Wilson estimate: 118.6 Å2 / Rmerge(I) obs: 0.214 / Net I/σ(I): 7.7
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 8.6 % / Rmerge(I) obs: 2.181 / Mean I/σ(I) obs: 1.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1760)refinement
Aimlessdata scaling
XDSdata scaling
SHELXphasing
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: SAD SOLUTION

Resolution: 3.5→48.799 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / Phase error: 28.17
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 1738 2.83 %random selection
Rwork0.2243 ---
obs0.2253 61399 99.96 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 118.1 Å2
Refinement stepCycle: LAST / Resolution: 3.5→48.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16336 0 2 0 16338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d016615
X-RAY DIFFRACTIONf_angle_d0.722442
X-RAY DIFFRACTIONf_dihedral_angle_d11.616151
X-RAY DIFFRACTIONf_chiral_restr0.022613
X-RAY DIFFRACTIONf_plane_restr02854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.6030.35721370.30094921X-RAY DIFFRACTION100
3.603-3.71920.33571470.29734904X-RAY DIFFRACTION100
3.7192-3.85210.34091460.28134929X-RAY DIFFRACTION100
3.8521-4.00630.28691420.25694940X-RAY DIFFRACTION100
4.0063-4.18850.29481430.22374938X-RAY DIFFRACTION100
4.1885-4.40920.24791440.20284920X-RAY DIFFRACTION100
4.4092-4.68520.20771430.18824965X-RAY DIFFRACTION100
4.6852-5.04670.25191460.18554944X-RAY DIFFRACTION100
5.0467-5.55390.23821450.20734964X-RAY DIFFRACTION100
5.5539-6.3560.27331460.24565018X-RAY DIFFRACTION100
6.356-8.00220.25681440.24665017X-RAY DIFFRACTION100
8.0022-48.80320.23171550.20795201X-RAY DIFFRACTION100
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)
10.7696-0.31850.06360.12770.5074-0.0763-0.0694-0.0740.12370.27190.01860.49370.21940.2333-00.9150.09390.20390.613-0.05470.7063-13.1297-72.977683.1367
2-0.8018-0.9272-0.20670.9771-0.41140.12620.0931-0.36190.04790.0822-0.01650.01230.06350.030600.58780.03030.08531.0142-0.16750.52266.9548-98.775470.4728
3-0.3376-0.269-0.4915-0.1729-0.0838-0.07331.1728-1.64681.5454-0.6579-0.95551.0890.2427-0.270800.8540.5791-0.2429-0.1120.17920.3505-17.3471-48.11966.8204
40.06990.2692-0.53530.34630.59330.25070.1347-0.1701-0.1999-0.17550.15910.1767-0.1078-0.5501-00.33930.15810.09330.2448-0.12850.3536-10.4004-64.642949.5538
50.34810.0285-0.0746-0.5043-0.27260.7396-0.0962-0.2450.221-0.13080.1468-0.1810.1010.270500.68590.07220.14090.6179-0.19560.8937-13.2308-44.54984.8702
6-0.09620.5792-0.6353-0.03870.241-0.3071-0.5270.10430.7641-0.27871.1364-0.38230.485-1.549-00.48770.18820.3116-0.081-0.47581.2677-6.9316-25.363984.6506
7-0.2464-0.0707-0.61020.21830.07580.05-0.65010.03150.7790.53680.83430.55350.50490.70201.35850.688-0.01390.9946-0.55340.477610.0431-77.056696.5182
81.2489-0.7564-0.4460.8278-0.61240.83570.00230.02670.03610.09090.00980.0902-0.125-0.0684-00.4198-0.0324-0.07820.4378-0.04440.404-2.2493-84.502127.4491
9-0.6989-0.9573-0.0179-0.02260.0811-0.6472-0.00830.159-0.44450.13610.3549-0.82180.2698-0.0548-00.4891-0.08830.16440.45590.07430.247412.7842-61.354224.8386
10-0.3938-0.2693-1.00310.4036-0.0527-0.02680.0701-0.41580.5287-0.06590.22810.05510.27410.157400.8039-0.0084-0.07440.5249-0.13230.930614.3641-50.891443.8185
110.1909-0.00430.56060.3024-0.17310.03820.0461-0.29850.3008-0.08110.14-0.0053-0.02270.170500.54760.1925-0.01240.7521-0.31990.914616.5152-62.744273.6894
120.80270.20940.04910.0249-0.71480.09010.1399-0.5030.1495-0.0731-0.077-0.076-0.10170.1561-00.82790.0255-0.22131.2163-0.11690.763238.1996-100.300571.6497
130.2212-0.56580.50490.3617-0.48550.7221-0.0049-0.0677-0.0477-0.15310.0618-0.0286-0.04910.0214-00.26960.0298-0.03910.4299-0.08760.434830.3475-111.804444.9313
14-0.0957-0.2106-0.1039-0.13610.1311-0.25570.02740.58240.6667-0.44230.38470.2404-0.39511.347401.42650.3314-0.01371.5946-0.17870.818420.6203-68.425989.4486
150.03790.073-0.01320.183-0.01520.00510.10310.03090.2663-0.04590.013-0.1066-0.2924-0.1162-0.00021.26690.4233-0.47771.9281-1.0612.260225.4799-88.629796.3783
160.07950.01120.01150.02140.01850.00120.00130.1904-0.1410.00020.23450.6250.035-0.0005-0.00021.4631.1262-0.03290.3604-1.10092.381613.8138-96.89897.8256
170.0111-0.0169-0.01830.05150.03360.03360.3052-0.1048-0.1321-0.1366-0.1558-0.01230.09910.0357-01.3534-0.1732-0.0731.27160.61211.51640.5482-95.083101.2803
180.0127-0.10490.0848-0.02130.0233-0.0031-0.4761-0.6458-0.2582-0.3695-0.1810.0350.5074-0.6827-02.7105-0.0047-0.42441.5161-0.10121.1358-18.2306-37.4867118.0357
19-0.1552-0.6513-0.12580.285-0.38570.4198-0.13570.083-0.0826-0.02220.01130.16710.0509-0.065500.403-0.04370.02670.5088-0.07330.4211-5.5615-111.407630.7194
200.1987-0.4270.42710.17180.0396-0.1474-0.0366-0.0366-0.10240.2243-0.0253-0.06590.05260.1307-00.4963-0.06410.00330.50890.01640.437-2.8364-114.455745.4559
21-0.3931-0.4898-0.355-0.0309-0.69160.24290.00820.1576-0.0610.13910.08660.0385-0.10070.061700.466-0.02520.05360.5195-0.02030.43193.2758-110.192619.6847
220.6142-0.3712-0.0340.3574-0.46540.06910.04550.2420.30550.0646-0.0796-0.02720.24840.163900.40580.0099-0.00940.7319-0.06690.430317.7694-97.605813.9105
230.2656-0.00170.37240.5809-0.65240.66720.0349-0.0195-0.09770.1478-0.1011-0.2852-0.0614-0.142400.5247-0.0521-0.06050.4898-0.07170.566227.0648-71.054442.335
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 326 through 497 )
2X-RAY DIFFRACTION2chain 'B' and (resid 498 through 616 )
3X-RAY DIFFRACTION3chain 'C' and (resid 46 through 88 )
4X-RAY DIFFRACTION4chain 'C' and (resid 89 through 252 )
5X-RAY DIFFRACTION5chain 'C' and (resid 253 through 381 )
6X-RAY DIFFRACTION6chain 'C' and (resid 382 through 598 )
7X-RAY DIFFRACTION7chain 'C' and (resid 599 through 721 )
8X-RAY DIFFRACTION8chain 'E' and (resid 1 through 159 )
9X-RAY DIFFRACTION9chain 'E' and (resid 160 through 243 )
10X-RAY DIFFRACTION10chain 'E' and (resid 244 through 337 )
11X-RAY DIFFRACTION11chain 'E' and (resid 338 through 458 )
12X-RAY DIFFRACTION12chain 'A' and (resid 569 through 737 )
13X-RAY DIFFRACTION13chain 'A' and (resid 738 through 919 )
14X-RAY DIFFRACTION14chain 'G' and (resid 1 through 19 )
15X-RAY DIFFRACTION15chain 'G' and (resid 20 through 24 )
16X-RAY DIFFRACTION16chain 'G' and (resid 25 through 34 )
17X-RAY DIFFRACTION17chain 'G' and (resid 35 through 41 )
18X-RAY DIFFRACTION18chain 'F' and (resid 223 through 241 )
19X-RAY DIFFRACTION19chain 'D' and (resid 5 through 132 )
20X-RAY DIFFRACTION20chain 'D' and (resid 133 through 197 )
21X-RAY DIFFRACTION21chain 'D' and (resid 198 through 264 )
22X-RAY DIFFRACTION22chain 'D' and (resid 265 through 332 )
23X-RAY DIFFRACTION23chain 'D' and (resid 333 through 457 )

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