PDB-2c38: RNase PH core of the archaeal exosome in complex with A5 RNA

ID or keywords:

Entry

Database: PDB / ID: 2c38

Title

RNase PH core of the archaeal exosome in complex with A5 RNA

Components

PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

Keywords

HYDROLASE / EXOSOME /

RNASE PH / RRP41 / RRP42 / PHOSPHOROLYTIC /

EXORIBONUCLEASE / RNA DEGRADATION /

ARCHAEAL /

EXONUCLEASE /

NUCLEASE

Function / homology

Function and homology information

cytoplasmic exosome (RNase complex) / rRNA catabolic process /

Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity
Similarity search - Function

Biological species

SULFOLOBUS SOLFATARICUS (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Lorentzen, E. / Conti, E.

Citation

Journal: Mol.Cell / Year: 2005
Title: Structural Basis of 3' End RNA Recognition and Exoribonucleolytic Cleavage by an Exosome Rnase Ph Core.
Authors: Lorentzen, E. / Conti, E.

History

Deposition	Oct 4, 2005	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 23, 2005	Provider: repository / Type: Initial release
Revision 1.1	May 7, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2c38.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb2c38.ent.gz	933 KB	Display	PDB format
PDBx/mmJSON format	2c38.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c3/2c38 ftp://data.pdbj.org/pub/pdb/validation_reports/c3/2c38	HTTPS FTP

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Related structure data

Related structure data	2c37C 2c39C 2br2S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2c37-1 2c39-2 2c37-2 2br2-1 2c37-4 2br2-2 2br2-3 2c39-4 2c39-1 2br2-4 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) 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

2c37C

2c39C

2br2S

S: Starting model for refinement

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	#86 - Feb 2007 Exosomes similarity (11) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

B: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

C: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

D: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

E: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

F: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

G: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

H: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

I: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

J: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

K: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

L: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

M: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

N: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

O: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

P: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

Q: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

R: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

S: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

T: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

U: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

V: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

W: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

X: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

hetero molecules

704 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

B: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

C: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

D: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

E: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

F: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

hetero molecules

defined by author&software
176 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

H: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

I: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

J: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

K: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

L: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

hetero molecules

defined by author&software
176 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

M: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

N: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

O: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

P: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

Q: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

R: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

hetero molecules

defined by author&software
175 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

S: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

T: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

U: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

V: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

W: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

X: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

hetero molecules

defined by author&software
176 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	206.260, 213.610, 434.040
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:
NCS ensembles :

ID
1
2
3

#1: Protein	PROBABLE EXOSOME COMPLEX EXONUCLEASE 2 Mass: 30227.625 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9UXC0, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Protein	PROBABLE EXOSOME COMPLEX EXONUCLEASE 1 Mass: 27612.936 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9UXC2, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	... ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate Mass: 347.221 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Comment: AMP*YM

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.4 Å³/Da / Density % sol: 63 %
Crystal grow	pH: 7 / Details: 50 MM MES, 2.4 M SODIUM MALONATE, PH 7.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.951
Detector	Type: MARRESEARCH / Detector: CCD / Date: Apr 17, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.951 Å / Relative weight: 1
Reflection	Resolution: 3.1→100 Å / Num. obs: 164956 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / R_merge(I) obs: 0.21 / Net I/σ(I): 8.4
Reflection shell	Resolution: 3.1→3.3 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.62 / Mean I/σ(I) obs: 2.6 / % possible all: 91.6

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BR2

2br2

Resolution: 3.1→95.78 Å / Cor.coef. F_o:F_c: 0.859 / Cor.coef. F_o:F_c free: 0.853 / SU B: 61.631 / SU ML: 0.45 / Cross valid method: THROUGHOUT / ESU R Free: 0.486 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.289	5102	3 %	RANDOM
R_work	0.276	-	-	-
obs	0.276	164956	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 58.26 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.08 Å²	0 Å²	0 Å²
2-	-	1.42 Å²	0 Å²
3-	-	-	0.66 Å²

Refinement step

Cycle: LAST / Resolution: 3.1→95.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	46983	0	635	0	47618

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	48401
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.202	2.013	65817
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.173	5	6136
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.035	24.822	1856
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.465	15	8495
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.96	15	288
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	7872
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	35352
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	21651
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.307	0.2	32462
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	1568
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	0.258	0.2	166
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.221	0.2	19
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	0.364	1.5	31380
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.656	2	49684
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.744	3	18884
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.374	4.5	16133
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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	1772	tight positional	0.03	0.05
1	2	C	1772	tight positional	0.03	0.05
1	3	E	1772	tight positional	0.03	0.05
1	4	G	1772	tight positional	0.03	0.05
1	5	I	1772	tight positional	0.03	0.05
1	6	K	1772	tight positional	0.03	0.05
1	7	M	1772	tight positional	0.03	0.05
1	8	O	1772	tight positional	0.03	0.05
1	9	Q	1772	tight positional	0.03	0.05
1	10	S	1772	tight positional	0.03	0.05
1	11	U	1772	tight positional	0.03	0.05
1	12	W	1772	tight positional	0.03	0.05
2	1	B	1736	tight positional	0.03	0.05
2	2	D	1736	tight positional	0.03	0.05
2	3	F	1736	tight positional	0.03	0.05
2	4	H	1736	tight positional	0.03	0.05
2	5	J	1736	tight positional	0.03	0.05
2	6	L	1736	tight positional	0.04	0.05
2	7	N	1736	tight positional	0.03	0.05
2	8	P	1736	tight positional	0.03	0.05
2	9	R	1736	tight positional	0.03	0.05
2	10	T	1736	tight positional	0.03	0.05
2	11	V	1736	tight positional	0.03	0.05
2	12	X	1736	tight positional	0.03	0.05
3	1	D	69	tight positional	0.04	0.05
3	2	L	69	tight positional	0.06	0.05
3	3	P	69	tight positional	0.05	0.05
3	4	R	69	tight positional	0.03	0.05
3	5	T	69	tight positional	0.04	0.05
1	1	A	1772	tight thermal	0.04	0.5
1	2	C	1772	tight thermal	0.04	0.5
1	3	E	1772	tight thermal	0.04	0.5
1	4	G	1772	tight thermal	0.04	0.5
1	5	I	1772	tight thermal	0.04	0.5
1	6	K	1772	tight thermal	0.04	0.5
1	7	M	1772	tight thermal	0.04	0.5
1	8	O	1772	tight thermal	0.04	0.5
1	9	Q	1772	tight thermal	0.04	0.5
1	10	S	1772	tight thermal	0.04	0.5
1	11	U	1772	tight thermal	0.04	0.5
1	12	W	1772	tight thermal	0.04	0.5
2	1	B	1736	tight thermal	0.04	0.5
2	2	D	1736	tight thermal	0.04	0.5
2	3	F	1736	tight thermal	0.04	0.5
2	4	H	1736	tight thermal	0.04	0.5
2	5	J	1736	tight thermal	0.04	0.5
2	6	L	1736	tight thermal	0.04	0.5
2	7	N	1736	tight thermal	0.04	0.5
2	8	P	1736	tight thermal	0.04	0.5
2	9	R	1736	tight thermal	0.04	0.5
2	10	T	1736	tight thermal	0.04	0.5
2	11	V	1736	tight thermal	0.04	0.5
2	12	X	1736	tight thermal	0.04	0.5
3	1	D	69	tight thermal	0.03	0.5
3	2	L	69	tight thermal	0.04	0.5
3	3	P	69	tight thermal	0.05	0.5
3	4	R	69	tight thermal	0.04	0.5
3	5	T	69	tight thermal	0.03	0.5

LS refinement shell

Resolution: 3.1→3.18 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.424	307
R_work	0.407	9951

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