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Found 1 Document (0.745 seconds)

BMRB: 19959

4CYK

Structural basis for binding of Pan3 to Pan2 and its function in mRNA recruitment and deadenylation

Authors

Wolf, J., Valkov, E., Allen, M.D., Meineke, B., Gordiyenko, Y., Mclaughlin, S.H., Olsen, T.M., Robinson, C.V., Bycroft, M., Stewart, M., Passmore, L.A., Olsen, S.

Assembly

Structural basis for binding of Pan3 to Pan2 and its function in mRNA recruitment and deadenylation

Entity

1. PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUN (polymer, Thiol state: all other bound), 41 monomers, 4733.338 Da Detail

MDKINPDWAK DIPCRNITIY GYCKKEKEGC PFKHSDNTTA T

2. Structural basis for binding of Pan3 to Pan2 and its function in mRNA recruitment and deadenylation, entity ZN (non-polymer), 65.409 Da

Total weight

4798.747 Da

Max. entity weight

4733.338 Da

Entity Connection

metal coordination 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	1:CYS14:SG	2:ZN1:ZN
2	metal coordination	sing	1:CYS23:SG	2:ZN1:ZN
3	metal coordination	sing	1:CYS30:SG	2:ZN1:ZN

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

CNS 1.2

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 85.8 %, Completeness (bb): 99.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.8 % (416 of 485)	99.6 % (255 of 256)	66.3 % (124 of 187)	88.1 % (37 of 42)
Backbone	99.6 % (239 of 240)	100.0 % (81 of 81)	100.0 % (121 of 121)	97.4 % (37 of 38)
Sidechain	76.1 % (216 of 284)	99.4 % (174 of 175)	40.0 % (42 of 105)	0.0 % (0 of 4)
Aromatic	50.0 % (21 of 42)	100.0 % (21 of 21)	0.0 % (0 of 20)	0.0 % (0 of 1)
Methyl	57.1 % (16 of 28)	100.0 % (14 of 14)	14.3 % (2 of 14)

1. PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUN

MDKINPDWAK DIPCRNITIY GYCKKEKEGC PFKHSDNTTA T

Show sample condition

Sample

Solvent system 90% water / 10% D2O, Pressure 1 atm, Temperature 293.000 K, pH 7.000, Details 1.5mM

#	Name	Isotope labeling	Concentration
1	PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUN	[U-13C; U-15N]	1.5 mM
2	Tris	natural abundance	20 mM
3	NaCl	natural abundance	100 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹⁵N	Dioxane	urea amide	77.5 ppm	external	indirect	1.0
¹³C	TSP	methyl carbons	0.0 ppm	external	indirect	1.0
¹H	TSP	methyl protons	0.0 ppm	external	indirect	1.0

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹⁵N	Dioxane	urea amide	77.5 ppm	external	indirect	1.0
¹³C	TSP	methyl carbons	0.0 ppm	external	indirect	1.0
¹H	TSP	methyl protons	0.0 ppm	external	indirect	1.0

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹⁵N	Dioxane	urea amide	77.5 ppm	external	indirect	1.0
¹³C	TSP	methyl carbons	0.0 ppm	external	indirect	1.0
¹H	TSP	methyl protons	0.0 ppm	external	indirect	1.0

Referencing offset: 0.01 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹⁵N	Dioxane	urea amide	77.5 ppm	external	indirect	1.0
¹³C	TSP	methyl carbons	0.0 ppm	external	indirect	1.0
¹H	TSP	methyl protons	0.0 ppm	external	indirect	1.0

Referencing offset: 1.14 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 4CYK, Strand ID: A Detail

Release date

2014-05-19

Citation

Structural basis for Pan3 binding to Pan2 and its function in mRNA recruitment and deadenylation
Wolf, J., Valkov, E., Allen, M.D., Meineke, B., Gordiyenko, Y., Mclaughlin, S.H., Olsen, T.M., Robinson, C.V., Bycroft, M., Stewart, M., Passmore, L.A.
EMBO J. (2014), 33, 1514-1526, PubMed 24872509 , DOI 10.15252/embj.201488373 , Abstract

Related entities 1. PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUN, : 1 : 2 : 9 entities Detail

Interaction partners 1. PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUN, : 13 interactors Detail

More details for 13 interactors identified by 2 citations

Experiments performed 1 experiments Detail

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19959_4cyk.nef
Input source #2: Coordindates	4cyk.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
2:1:ZN:ZN	1:14:CYS:SG	unknown	unknown	n/a
2:1:ZN:ZN	1:23:CYS:SG	unknown	unknown	n/a
2:1:ZN:ZN	1:30:CYS:SG	unknown	unknown	n/a
2:1:ZN:ZN	1:34:HIS:NE2	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40-
MDKINPDWAKDIPCRNITIYGYCKKEKEGCPFKHSDNTTAT
|||||||||||||||||||||||||||||||||||||||||
MDKINPDWAKDIPCRNITIYGYCKKEKEGCPFKHSDNTTAT

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	41	0	0	100.0

Content subtype: combined_19959_4cyk.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	412		100.0 (chain: A, length: 41)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1380 (1)	noe	100.0 (chain: A, length: 41)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	6 (1)	undefined	9.8 (chain: A, length: 41)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	8 (1)	hbond	17.1 (chain: A, length: 41)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	Warning	8 (8)	.	19.5 (chain: A, length: 41)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_6	OK	62 (62)	.	85.4 (chain: A, length: 41)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 255
  - ¹³C chemical shifts: 121
  - ¹⁵N chemical shifts: 36
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	256	254	99.2
¹³C chemical shifts	187	121	64.7
¹⁵N chemical shifts	43	36	83.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	81	80	98.8
¹³C chemical shifts	82	82	100.0
¹⁵N chemical shifts	38	36	94.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	175	174	99.4
¹³C chemical shifts	105	39	37.1
¹⁵N chemical shifts	5	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	15	100.0
¹³C chemical shifts	15	2	13.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	21	21	100.0
¹³C chemical shifts	20	0	0.0
¹⁵N chemical shifts	1	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 100.0%
- Total number of restraints: 1374
- Weight of restraints: 1.0 (1374)
- Potential type of restraints: square-well-parabolic (1374)
- Range of distance target values: 2.65, 3.9 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 9.8%
  - Total number of restraints: 6
  - Weight of restraints: 1.0 (6)
  - Potential type of restraints: square-well-parabolic (6)
  - Range of distance target values: 3.45, 3.75 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_4
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 17.1%
    - Total number of restraints: 8
    - Weight of restraints: 1.0 (8)
    - Potential type of restraints: square-well-parabolic (8)
    - Range of distance target values: 1.95, 2.9 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_5
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 19.5%
- Total number of restraints: 8
- Total number of restraints per polymer type: 8
- Weight of restraints: 1.0 (8)
- Potential type of restraints: square-well-parabolic (8)
- Dihedral angle restraints per residue
- Saveframe: CNS/XPLOR_dihedral_6
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 85.4%
  - Total number of restraints: 62
  - Total number of restraints per polymer type: 62
  - Weight of restraints: 1.0 (62)
  - Potential type of restraints: square-well-parabolic (62)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A

Keywords Pan3p, Pan2p, polyA, RNA, deadenylation, TRANSCRIPTION

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Found 1 Document (0.745 seconds)

BMRB: 19959

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUN, : 1 : 2 : 9 entities Detail

Interaction partners 1. PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUN, : 13 interactors Detail

Experiments performed 1 experiments Detail

Instrument

Sample

NMR combined restraints 7 contents Detail