PDB-2hik: heterotrimeric PCNA sliding clamp

ID or keywords:

Entry

Database: PDB / ID: 2hik

Title

heterotrimeric PCNA sliding clamp

Components

PCNA1 (SSO0397)
PCNA2 (SSO1047)
PCNA3 (SSO0405)

Keywords

REPLICATION / PCNA sliding clamp / processivity factor / DNA replication / heterotrimer

Function / homology

Function and homology information

leading strand elongation / DNA polymerase processivity factor activity / regulation of DNA replication / DNA binding
Similarity search - Function

Biological species

Sulfolobus solfataricus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.3 Å

Authors

Pascal, J.M. / Tsodikov, O.V. / Ellenberger, T.

Citation

Journal: Mol.Cell / Year: 2006
Title: A Flexible Interface between DNA Ligase and PCNA Supports Conformational Switching and Efficient Ligation of DNA.
Authors: Pascal, J.M. / Tsodikov, O.V. / Hura, G.L. / Song, W. / Cotner, E.A. / Classen, S. / Tomkinson, A.E. / Tainer, J.A. / Ellenberger, T.

History

Deposition	Jun 29, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 7, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.4	Nov 20, 2024	Group: 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_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2hik.cif.gz	417.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2hik.ent.gz	342.6 KB	Display	PDB format
PDBx/mmJSON format	2hik.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2hik_validation.pdf.gz	500.6 KB	Display	wwPDB validaton report
Full document	2hik_full_validation.pdf.gz	545.6 KB	Display
Data in XML	2hik_validation.xml.gz	82.1 KB	Display
Data in CIF	2hik_validation.cif.gz	106.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hi/2hik ftp://data.pdbj.org/pub/pdb/validation_reports/hi/2hik	HTTPS FTP

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Related structure data

Related structure data	2hiiC 2hivC 2hixC C: citing same article (ref.)
Similar structure data	2hii-1 2hii-2 2nti-3 2nti-1 2nti-2 3lx2-d 5yco-1 5mlw-1 6k3a-d 3hi8-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

2hiiC

2hivC

2hixC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#150 - Jun 2012 Sliding Clamps similarity (7) #241 - Jan 2020 Twenty Years of Molecules similarity (7)

Deposited unit

A: PCNA1 (SSO0397)

B: PCNA2 (SSO1047)

C: PCNA3 (SSO0405)

L: PCNA1 (SSO0397)

M: PCNA2 (SSO1047)

N: PCNA3 (SSO0405)

X: PCNA1 (SSO0397)

Y: PCNA2 (SSO1047)

Z: PCNA3 (SSO0405)

256 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PCNA1 (SSO0397)

B: PCNA2 (SSO1047)

C: PCNA3 (SSO0405)

defined by author&software
85.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

L: PCNA1 (SSO0397)

M: PCNA2 (SSO1047)

N: PCNA3 (SSO0405)

defined by author&software
85.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

X: PCNA1 (SSO0397)

Y: PCNA2 (SSO1047)

Z: PCNA3 (SSO0405)

defined by author&software
85.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	142.275, 223.093, 79.140
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	LYS	LYS	THR	THR	4	A	A	3 - 112	3 - 112
2	1	1	LYS	LYS	THR	THR	4	L	D	3 - 112	3 - 112
3	1	1	LYS	LYS	THR	THR	4	X	G	3 - 112	3 - 112
4	2	1	THR	THR	ALA	ALA	4	A	A	138 - 170	138 - 170
5	2	1	THR	THR	ALA	ALA	4	L	D	138 - 170	138 - 170
6	2	1	THR	THR	ALA	ALA	4	X	G	138 - 170	138 - 170
7	3	1	GLY	GLY	ARG	ARG	6	A	A	171 - 176	171 - 176
8	3	1	GLY	GLY	ARG	ARG	6	L	D	171 - 176	171 - 176
9	3	1	GLY	GLY	ARG	ARG	6	X	G	171 - 176	171 - 176
10	4	1	TYR	TYR	PRO	PRO	4	A	A	177 - 247	177 - 247
11	4	1	TYR	TYR	PRO	PRO	4	L	D	177 - 247	177 - 247
12	4	1	TYR	TYR	PRO	PRO	4	X	G	177 - 247	177 - 247
13	5	1	ILE	ILE	THR	THR	6	A	A	113 - 137	113 - 137
14	5	1	ILE	ILE	THR	THR	6	L	D	113 - 137	113 - 137
15	5	1	ILE	ILE	THR	THR	6	X	G	113 - 137	113 - 137
1	1	2	ALA	ALA	SER	SER	4	B	B	4 - 109	3 - 108
2	1	2	ALA	ALA	SER	SER	4	M	E	4 - 109	3 - 108
3	1	2	ALA	ALA	SER	SER	4	Y	H	4 - 109	3 - 108
4	2	2	LEU	LEU	LEU	LEU	4	B	B	136 - 231	135 - 230
5	2	2	LEU	LEU	LEU	LEU	4	M	E	136 - 231	135 - 230
6	2	2	LEU	LEU	LEU	LEU	4	Y	H	136 - 231	135 - 230
7	3	2	PHE	PHE	LEU	LEU	6	B	B	110 - 135	109 - 134
8	3	2	PHE	PHE	LEU	LEU	6	M	E	110 - 135	109 - 134
9	3	2	PHE	PHE	LEU	LEU	6	Y	H	110 - 135	109 - 134
10	4	2	PRO	PRO	GLY	GLY	6	B	B	232 - 235	231 - 234
11	4	2	PRO	PRO	GLY	GLY	6	M	E	232 - 235	231 - 234
12	4	2	PRO	PRO	GLY	GLY	6	Y	H	232 - 235	231 - 234
13	5	2	TYR	TYR	PRO	PRO	4	B	B	236 - 243	235 - 242
14	5	2	TYR	TYR	PRO	PRO	4	M	E	236 - 243	235 - 242
15	5	2	TYR	TYR	PRO	PRO	4	Y	H	236 - 243	235 - 242
1	1	3	VAL	VAL	LEU	LEU	4	C	C	3 - 39	3 - 39
2	1	3	VAL	VAL	LEU	LEU	4	N	F	3 - 39	3 - 39
3	1	3	VAL	VAL	LEU	LEU	4	Z	I	3 - 39	3 - 39
4	2	3	ASP	ASP	ALA	ALA	6	C	C	40 - 42	40 - 42
5	2	3	ASP	ASP	ALA	ALA	6	N	F	40 - 42	40 - 42
6	2	3	ASP	ASP	ALA	ALA	6	Z	I	40 - 42	40 - 42
7	3	3	HIS	HIS	GLU	GLU	4	C	C	43 - 108	43 - 108
8	3	3	HIS	HIS	GLU	GLU	4	N	F	43 - 108	43 - 108
9	3	3	HIS	HIS	GLU	GLU	4	Z	I	43 - 108	43 - 108
10	4	3	PHE	PHE	ILE	ILE	6	C	C	109 - 134	109 - 134
11	4	3	PHE	PHE	ILE	ILE	6	N	F	109 - 134	109 - 134
12	4	3	PHE	PHE	ILE	ILE	6	Z	I	109 - 134	109 - 134
13	5	3	SER	SER	ALA	ALA	4	C	C	135 - 241	135 - 241
14	5	3	SER	SER	ALA	ALA	4	N	F	135 - 241	135 - 241
15	5	3	SER	SER	ALA	ALA	4	Z	I	135 - 241	135 - 241

NCS ensembles :

ID
1
2
3

#1: Protein	PCNA1 (SSO0397) / DNA polymerase sliding clamp B / Proliferating cell nuclear antigen homolog B / PCNA B Mass: 29062.934 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: pcnB, pcnA-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P57766
#2: Protein	PCNA2 (SSO1047) / DNA polymerase sliding clamp C / Proliferating cell nuclear antigen homolog C / PCNA C Mass: 27648.662 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: pcnC, pcnA-2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97Z84
#3: Protein	PCNA3 (SSO0405) / DNA polymerase sliding clamp A / Proliferating cell nuclear antigen homolog A / PCNA A Mass: 28747.846 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: pcnA, pcnA-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P57765
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.51 Å³/Da / Density % sol: 50.99 %
Crystal grow	Temperature: 298 K / pH: 5.5 Details: 18-20% PEG 3350, 150mM ammonium citrate, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 5.50

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.98
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 3.3→50 Å / Num. obs: 35317 / % possible obs: 88.6 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / R_merge(I) obs: 0.1 / Net I/σ(I): 8.2
Reflection shell	Resolution: 3.3→3.42 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.309 / Mean I/σ(I) obs: 2.1 / % possible all: 84.2

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	2	data extraction
PHASES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.3→20 Å / Cor.coef. F_o:F_c: 0.902 / Cor.coef. F_o:F_c free: 0.842 / SU B: 87.795 / SU ML: 0.635 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.763 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.299	1750	5.1 %	RANDOM
R_work	0.236	-	-	-
obs	0.239	34234	88.8 %	-
all	-	34234	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 71.73 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.98 Å²	0 Å²	0 Å²
2-	-	4.5 Å²	0 Å²
3-	-	-	-1.52 Å²

Refinement step

Cycle: LAST / Resolution: 3.3→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17311	0	0	0	17311

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	17578
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.035	1.981	23714
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5	5	2195
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.207	25.412	765
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.761	15	3309
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.439	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	2777
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	12851
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.192	0.2	8566
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.306	0.2	11748
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.135	0.2	689
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.196	0.2	168
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.144	0.2	13
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.211	1.5	11273
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.298	2	17819
X-RAY DIFFRACTION	r_scbond_it	0.418	3	6961
X-RAY DIFFRACTION	r_scangle_it	0.606	4.5	5895
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1644	medium positional	0.17	0.2
1	2	L	1644	medium positional	0.12	0.2
1	3	X	1644	medium positional	0.15	0.2
2	1	B	1655	medium positional	0.19	0.2
2	2	M	1655	medium positional	0.15	0.2
2	3	Y	1655	medium positional	0.16	0.2
3	1	C	1657	medium positional	0.2	0.2
3	2	N	1657	medium positional	0.13	0.2
3	3	Z	1657	medium positional	0.15	0.2
1	1	A	245	loose positional	0.93	10
1	2	L	245	loose positional	1.03	10
1	3	X	245	loose positional	0.73	10
2	1	B	239	loose positional	1.08	10
2	2	M	239	loose positional	0.99	10
2	3	Y	239	loose positional	0.82	10
3	1	C	236	loose positional	1.56	10
3	2	N	236	loose positional	0.94	10
3	3	Z	236	loose positional	1.32	10
1	1	A	1644	medium thermal	0.15	2
1	2	L	1644	medium thermal	0.16	2
1	3	X	1644	medium thermal	0.13	2
2	1	B	1655	medium thermal	0.15	2
2	2	M	1655	medium thermal	0.15	2
2	3	Y	1655	medium thermal	0.16	2
3	1	C	1657	medium thermal	0.14	2
3	2	N	1657	medium thermal	0.12	2
3	3	Z	1657	medium thermal	0.13	2
1	1	A	245	loose thermal	0.59	10
1	2	L	245	loose thermal	0.79	10
1	3	X	245	loose thermal	0.8	10
2	1	B	239	loose thermal	0.83	10
2	2	M	239	loose thermal	0.74	10
2	3	Y	239	loose thermal	0.94	10
3	1	C	236	loose thermal	1.01	10
3	2	N	236	loose thermal	0.28	10
3	3	Z	236	loose thermal	0.96	10

LS refinement shell

Resolution: 3.3→3.38 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.358	117	-
R_work	0.278	2131	-
obs	-	-	82.16 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	5.72	-3.1386	-0.6521	2.9794	0.1047	3.2233	-0.2276	-0.1056	-0.1031	-0.0445	-0.1255	-0.1158	0.4456	0.7266	0.353	-0.0586	-0.0077	-0.0627	-0.1178	-0.0304	-0.3841	46.4523	-18.1595	-14.1575
2	1.1235	0.9163	-0.3836	1.5087	-1.7292	9.072	-0.1602	0.1606	0.3652	0.0502	0.0208	0.1503	-0.2234	-0.4428	0.1394	-0.3472	0.1308	-0.1624	-0.5492	0.0056	-0.1814	25.4393	7.25	-41.8153
3	6.9948	-4.6383	5.5756	5.2947	-4.647	8.6211	-0.0423	0.2855	-0.082	-0.237	0.1719	0.0743	0.1815	0.6002	-0.1296	-0.2849	0.1021	0.0919	-0.1657	0.0194	-0.4586	58.5053	-15.7328	-54.6772
4	7.5013	-3.2512	-1.0069	3.3243	1.29	4.3491	0.1512	0.1035	0.2861	-0.2651	-0.229	0.0671	-0.3205	-0.8342	0.0778	0.0488	0.0582	-0.1833	-0.0636	0.0736	0.0092	-21.0983	37.1377	-21.663
5	3.2024	0.1229	-1.6356	1.4637	-1.1224	7.5536	-0.0543	-0.4926	-0.4906	-0.0477	-0.2499	0.1015	0.3323	0.177	0.3042	-0.4282	-0.0422	-0.2288	-0.4479	0.1327	0.3615	0.6328	16.3745	8.9784
6	5.0005	-3.0274	2.6458	5.5151	-3.7431	7.4735	0.0972	0.3177	-0.3794	0.1065	-0.1698	0.3628	-0.0569	-1.3356	0.0726	-0.3052	-0.0209	-0.1047	0.1889	-0.4134	0.0706	-34.4365	37.2076	18.8889
7	5.0334	3.1269	-1.0445	3.9055	-2.0367	4.1959	0.2016	0.3839	0.1399	0.2056	0.3235	-0.1392	-0.407	0.4751	-0.5251	-0.1826	0.0988	-0.0109	-0.1764	-0.2331	-0.3231	62.7211	44.8338	15.1959
8	1.7693	-0.4407	1.0763	2.4501	-0.4499	7.7714	0.3067	-0.3055	-0.2329	-0.0501	0.0817	-0.0076	0.0571	0.0054	-0.3884	-0.4868	-0.0039	-0.1568	-0.522	0.0336	-0.1807	33.5045	30.7572	-12.0893
9	6.6919	2.3656	5.3132	4.5924	3.3958	8.4153	0.1892	-0.0096	0.1268	-0.1752	-0.1167	-0.1484	-0.1632	0.9311	-0.0726	-0.2514	0.0259	0.2416	-0.1617	-0.1	-0.3368	64.1983	57.2422	-25.1496

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	2 - 250	2 - 250
2	X-RAY DIFFRACTION	2	B	B	2 - 245	1 - 244
3	X-RAY DIFFRACTION	3	C	C	1 - 243	1 - 243
4	X-RAY DIFFRACTION	4	L	D	2 - 249	2 - 249
5	X-RAY DIFFRACTION	5	M	E	2 - 244	1 - 243
6	X-RAY DIFFRACTION	6	N	F	1 - 243	1 - 243
7	X-RAY DIFFRACTION	7	X	G	2 - 249	2 - 249
8	X-RAY DIFFRACTION	8	Y	H	2 - 244	1 - 243
9	X-RAY DIFFRACTION	9	Z	I	1 - 243	1 - 243

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Movie

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Structure viewers

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Validation report

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Assembly

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Data collection

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi