PDB-2c39: RNase PH core of the archaeal exosome in complex with ADP

Basic information

• Entry: Database: PDB / ID: 2c39
• Title: RNase PH core of the archaeal exosome in complex with ADP

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:

cytoplasmic exosome (RNase complex) / rRNA catabolic process / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity

Domain/homology:

Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / GHMP Kinase, N-terminal domain / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta

Component:

ADENOSINE-5'-DIPHOSPHATE / Exosome complex component Rrp42 / Exosome complex component Rrp41

• Biological species: SULFOLOBUS SOLFATARICUS (archaea)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 5, 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 / Derived calculations / Other / Refinement description Category: 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 / _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 THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

Assembly

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

Summary:

• 699 kDa, 24 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	699,213	36
Polymers	694,087	24
Non-polymers	5,126	12
Water	0

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

Summary:

• defined by author&software
• 175 kDa, 6 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	174,803	9
Polymers	173,522	6
Non-polymers	1,282	3
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PQS

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

Summary:

• defined by author&software
• 175 kDa, 6 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	174,803	9
Polymers	173,522	6
Non-polymers	1,282	3
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PQS

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

Summary:

• defined by author&software
• 175 kDa, 6 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	174,803	9
Polymers	173,522	6
Non-polymers	1,282	3
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PQS

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

Summary:

• defined by author&software
• 175 kDa, 6 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	174,803	9
Polymers	173,522	6
Non-polymers	1,282	3
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PQS

Unit cell

Length a, b, c (Å)	206.200, 214.000, 432.500
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:

ID	Ens-ID	Details
1	1	A
2	1	C
3	1	E
4	1	G
5	1	I
6	1	K
7	1	M
8	1	O
9	1	Q
10	1	S
11	1	U
12	1	W
1	2	B
2	2	D
3	2	F
4	2	H
5	2	J
6	2	L
7	2	N
8	2	P
9	2	R
10	2	T
11	2	V
12	2	X
1	3	D
2	3	L
3	3	P
4	3	R
5	3	T

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	1 - 74
2	1	1	1	C	1 - 74
3	1	1	1	E	1 - 74
4	1	1	1	G	1 - 74
5	1	1	1	I	1 - 74
6	1	1	1	K	1 - 74
7	1	1	1	M	1 - 74
8	1	1	1	O	1 - 74
9	1	1	1	Q	1 - 74
10	1	1	1	S	1 - 74
11	1	1	1	U	1 - 74
12	1	1	1	W	1 - 74
1	2	1	1	A	76 - 121
2	2	1	1	C	76 - 121
3	2	1	1	E	76 - 121
4	2	1	1	G	76 - 121
5	2	1	1	I	76 - 121
6	2	1	1	K	76 - 121
7	2	1	1	M	76 - 121
8	2	1	1	O	76 - 121
9	2	1	1	Q	76 - 121
10	2	1	1	S	76 - 121
11	2	1	1	U	76 - 121
12	2	1	1	W	76 - 121
1	3	1	1	A	123 - 231
2	3	1	1	C	123 - 231
3	3	1	1	E	123 - 231
4	3	1	1	G	123 - 231
5	3	1	1	I	123 - 231
6	3	1	1	K	123 - 231
7	3	1	1	M	123 - 231
8	3	1	1	O	123 - 231
9	3	1	1	Q	123 - 231
10	3	1	1	S	123 - 231
11	3	1	1	U	123 - 231
12	3	1	1	W	123 - 231
1	4	1	1	A	233 - 275
2	4	1	1	C	233 - 275
3	4	1	1	E	233 - 275
4	4	1	1	G	233 - 275
5	4	1	1	I	233 - 275
6	4	1	1	K	233 - 275
7	4	1	1	M	233 - 275
8	4	1	1	O	233 - 275
9	4	1	1	Q	233 - 275
10	4	1	1	S	233 - 275
11	4	1	1	U	233 - 275
12	4	1	1	W	233 - 275
1	1	2	1	B	18 - 182
2	1	2	1	D	18 - 182
3	1	2	1	F	18 - 182
4	1	2	1	H	18 - 182
5	1	2	1	J	18 - 182
6	1	2	1	L	18 - 182
7	1	2	1	N	18 - 182
8	1	2	1	P	18 - 182
9	1	2	1	R	18 - 182
10	1	2	1	T	18 - 182
11	1	2	1	V	18 - 182
12	1	2	1	X	18 - 182
1	2	2	1	B	184 - 248
2	2	2	1	D	184 - 248
3	2	2	1	F	184 - 248
4	2	2	1	H	184 - 248
5	2	2	1	J	184 - 248
6	2	2	1	L	184 - 248
7	2	2	1	N	184 - 248
8	2	2	1	P	184 - 248
9	2	2	1	R	184 - 248
10	2	2	1	T	184 - 248
11	2	2	1	V	184 - 248
12	2	2	1	X	184 - 248
1	1	3	1	D	8 - 18
2	1	3	1	L	8 - 18
3	1	3	1	P	8 - 18
4	1	3	1	R	8 - 18
5	1	3	1	T	8 - 18

NCS ensembles :

ID
1
2
3

Components

#1: Protein

A C E G I K M O Q S U W
PROBABLE EXOSOME COMPLEX EXONUCLEASE 2

Details:

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

B D F H J L N P R T V X
PROBABLE EXOSOME COMPLEX EXONUCLEASE 1

Details:

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

B-404 D-404 F-404 H-404 J-404 L-404 N-404 P-404 R-404 T-404 V-404 X-404
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate

Details:

Mass: 427.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM

Experimental details

Experiment

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

Sample preparation

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

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: 3.3→100 Å / Num. obs: 129777 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / R_merge(I) obs: 0.18 / Net I/σ(I): 8.1
• Reflection shell: Resolution: 3.3→3.5 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.75 / Mean I/σ(I) obs: 2.4 / % possible all: 95.3

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 2BR3

2br3

Resolution: 3.3→93.25 Å / Cor.coef. F_o:F_c: 0.866 / Cor.coef. F_o:F_c free: 0.846 / SU B: 61.763 / SU ML: 0.457 / Cross valid method: THROUGHOUT / ESU R Free: 0.584 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.295	4015	3 %	RANDOM
Rwork	0.274	-	-	-
obs	0.275	129777	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: 54.17 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-0.02 Å2	0 Å2	0 Å2
2-	-	0.05 Å2	0 Å2
3-	-	-	-0.03 Å2

Refinement step

Cycle: LAST / Resolution: 3.3→93.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	45538	0	276	0	45814

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	46461
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.224	2.001	63079
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.919	5	5972
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.173	24.626	1736
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.688	15	8208
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.94	15	287
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	7612
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	33752
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.206	0.2	19816
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.306	0.2	31059
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.148	0.2	1423
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	0.234	0.2	163
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.279	0.2	20
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	0.376	1.5	30626
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.652	2	48300
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.831	3	17482
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.49	4.5	14779
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	1726	tight positional	0.03	0.05
1	2	C	1726	tight positional	0.04	0.05
1	3	E	1726	tight positional	0.03	0.05
1	4	G	1726	tight positional	0.03	0.05
1	5	I	1726	tight positional	0.03	0.05
1	6	K	1726	tight positional	0.04	0.05
1	7	M	1726	tight positional	0.03	0.05
1	8	O	1726	tight positional	0.04	0.05
1	9	Q	1726	tight positional	0.03	0.05
1	10	S	1726	tight positional	0.04	0.05
1	11	U	1726	tight positional	0.03	0.05
1	12	W	1726	tight positional	0.03	0.05
2	1	B	1480	tight positional	0.03	0.05
2	2	D	1480	tight positional	0.04	0.05
2	3	F	1480	tight positional	0.03	0.05
2	4	H	1480	tight positional	0.03	0.05
2	5	J	1480	tight positional	0.03	0.05
2	6	L	1480	tight positional	0.04	0.05
2	7	N	1480	tight positional	0.03	0.05
2	8	P	1480	tight positional	0.04	0.05
2	9	R	1480	tight positional	0.04	0.05
2	10	T	1480	tight positional	0.04	0.05
2	11	V	1480	tight positional	0.04	0.05
2	12	X	1480	tight positional	0.03	0.05
3	1	D	61	tight positional	0.04	0.05
3	2	L	61	tight positional	0.04	0.05
3	3	P	61	tight positional	0.04	0.05
3	4	R	61	tight positional	0.03	0.05
3	5	T	61	tight positional	0.04	0.05
1	1	A	1726	tight thermal	0.05	0.5
1	2	C	1726	tight thermal	0.05	0.5
1	3	E	1726	tight thermal	0.04	0.5
1	4	G	1726	tight thermal	0.05	0.5
1	5	I	1726	tight thermal	0.04	0.5
1	6	K	1726	tight thermal	0.05	0.5
1	7	M	1726	tight thermal	0.05	0.5
1	8	O	1726	tight thermal	0.06	0.5
1	9	Q	1726	tight thermal	0.05	0.5
1	10	S	1726	tight thermal	0.05	0.5
1	11	U	1726	tight thermal	0.04	0.5
1	12	W	1726	tight thermal	0.04	0.5
2	1	B	1480	tight thermal	0.04	0.5
2	2	D	1480	tight thermal	0.05	0.5
2	3	F	1480	tight thermal	0.05	0.5
2	4	H	1480	tight thermal	0.05	0.5
2	5	J	1480	tight thermal	0.04	0.5
2	6	L	1480	tight thermal	0.05	0.5
2	7	N	1480	tight thermal	0.05	0.5
2	8	P	1480	tight thermal	0.06	0.5
2	9	R	1480	tight thermal	0.05	0.5
2	10	T	1480	tight thermal	0.05	0.5
2	11	V	1480	tight thermal	0.05	0.5
2	12	X	1480	tight thermal	0.04	0.5
3	1	D	61	tight thermal	0.06	0.5
3	2	L	61	tight thermal	0.04	0.5
3	3	P	61	tight thermal	0.06	0.5
3	4	R	61	tight thermal	0.04	0.5
3	5	T	61	tight thermal	0.05	0.5

LS refinement shell

Resolution: 3.3→3.39 Å / Total num. of bins used: 20 /

	Rfactor	Num. reflection
Rfree	0.359	294
Rwork	0.344	9524