BMRBj - BMREntryMaster

Found 1 Document (2.119 seconds)

BMRB: 34200

6EZ4

NMR structure of the C-terminal domain of the human RPAP3 protein

Authors

Fabre, P., Chagot, M.E., Bragantini, B., Manival, X., Quinternet, M.

Assembly

RNA polymerase II-associated protein 3

Entity

1. RNA polymerase II-associated protein 3 (polymer, Thiol state: not present), 135 monomers, 15782.18 Da Detail

GPHMAQFATT VLPPIPANSF QLESDFRQLK SSPDMLYQYL KQIEPSLYPK LFQKNLDPDV FNQIVKILHD FYIEKEKPLL IFEILQRLSE LKRFDMAVMF MSETEKKIAR ALFNHIDKSG LKDSSVEELK KRYGG

Formula weight

15782.18 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.3 %, Completeness: 95.7 %, Completeness (bb): 98.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.7 % (1631 of 1704)	97.7 % (879 of 900)	92.3 % (615 of 666)	99.3 % (137 of 138)
Backbone	98.9 % (783 of 792)	98.1 % (260 of 265)	99.3 % (398 of 401)	99.2 % (125 of 126)
Sidechain	93.9 % (979 of 1043)	97.5 % (619 of 635)	87.9 % (348 of 396)	100.0 % (12 of 12)
Aromatic	62.5 % (95 of 152)	85.5 % (65 of 76)	39.5 % (30 of 76)
Methyl	100.0 % (142 of 142)	100.0 % (71 of 71)	100.0 % (71 of 71)

1. entity 1

GPHMAQFATT VLPPIPANSF QLESDFRQLK SSPDMLYQYL KQIEPSLYPK LFQKNLDPDV FNQIVKILHD FYIEKEKPLL IFEILQRLSE LKRFDMAVMF MSETEKKIAR ALFNHIDKSG LKDSSVEELK KRYGG

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4, Details 1 mM [U-13C; U-15N] RPAP3 C-terminal domain, 150 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM TCEP, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	RPAP3 C-terminal domain	[U-13C; U-15N]	1 mM
2	TCEP	natural abundance	0.5 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.32 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.32 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.34 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6EZ4, Strand ID: A Detail

Release date

2017-11-16

Citation

The RPAP3-Cterminal domain identifies R2TP-like quaternary chaperones
Maurizy, C., Quinternet, M., Abel, Y., Verheggen, C., Santo, P.E., Bourguet, M., C F Paiva, A., Bragantini, B., Chagot, M.E., Robert, M.C., Abeza, C., Fabre, P., Fort, P., Vandermoere, F., M F Sousa, P., Rain, J.C., Charpentier, B., Cianferani, S., Bandeiras, T.M., Pradet-Balade, B., Manival, X., Bertrand, E.
Nat. Commun. (2018), 9, 2093-2093, PubMed 29844425 , DOI 10.1038/s41467-018-04431-1 , Abstract

Related entities 1. RNA polymerase II-associated protein 3, : 1 : 3 : 20 entities Detail

Interaction partners 1. RNA polymerase II-associated protein 3, : 60 interactors Detail

More details for 60 interactors identified by 21 citations

Experiments performed 18 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4, Details 1 mM [U-13C; U-15N] RPAP3 C-terminal domain, 150 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM TCEP, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	RPAP3 C-terminal domain	[U-13C; U-15N]	1 mM
2	TCEP	natural abundance	0.5 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3 C-terminal domain	[U-13C; U-15N]	1 mM
2	TCEP	natural abundance	0.5 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM

3 2D 1H-13C HSQC aromatic

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3 C-terminal domain	[U-13C; U-15N]	1 mM
2	TCEP	natural abundance	0.5 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM

4 3D HNCA

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3 C-terminal domain	[U-13C; U-15N]	1 mM
2	TCEP	natural abundance	0.5 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM

5 3D HNCACB

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3 C-terminal domain	[U-13C; U-15N]	1 mM
2	TCEP	natural abundance	0.5 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM

6 2D 1H-1H NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3 C-terminal domain	[U-13C; U-15N]	1 mM
2	TCEP	natural abundance	0.5 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM

7 3D HBHA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3 C-terminal domain	[U-13C; U-15N]	1 mM
2	TCEP	natural abundance	0.5 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM

8 3D HCCH-COSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3 C-terminal domain	[U-13C; U-15N]	1 mM
2	TCEP	natural abundance	0.5 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM

9 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3 C-terminal domain	[U-13C; U-15N]	1 mM
2	TCEP	natural abundance	0.5 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM

10 3D (H)CCCONH

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3 C-terminal domain	[U-13C; U-15N]	1 mM
2	TCEP	natural abundance	0.5 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM

11 3D H(CCO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3 C-terminal domain	[U-13C; U-15N]	1 mM
2	TCEP	natural abundance	0.5 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM

12 3D HNHA

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3 C-terminal domain	[U-13C; U-15N]	1 mM
2	TCEP	natural abundance	0.5 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM

13 3D HNCO E.cosy

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3 C-terminal domain	[U-13C; U-15N]	1 mM
2	TCEP	natural abundance	0.5 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM

14 3D HNCACO

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3 C-terminal domain	[U-13C; U-15N]	1 mM
2	TCEP	natural abundance	0.5 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM

15 3D HNCO

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3 C-terminal domain	[U-13C; U-15N]	1 mM
2	TCEP	natural abundance	0.5 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM

16 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3 C-terminal domain	[U-13C; U-15N]	1 mM
2	TCEP	natural abundance	0.5 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM

17 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3 C-terminal domain	[U-13C; U-15N]	1 mM
2	TCEP	natural abundance	0.5 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM

18 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3 C-terminal domain	[U-13C; U-15N]	1 mM
2	TCEP	natural abundance	0.5 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34200_6ez4.nef
Input source #2: Coordindates	6ez4.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	None
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)

None

Non-standard residues

None

Sequence alignments

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

-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630
GPHMAQFATTVLPPIPANSFQLESDFRQLKSSPDMLYQYLKQIEPSLYPKLFQKNLDPDVFNQIVKILHDFYIEKEKPLLIFEILQRLSELKRFDMAVMF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPHMAQFATTVLPPIPANSFQLESDFRQLKSSPDMLYQYLKQIEPSLYPKLFQKNLDPDVFNQIVKILHDFYIEKEKPLLIFEILQRLSELKRFDMAVMF
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------640-------650-------660-----
MSETEKKIARALFNHIDKSGLKDSSVEELKKRYGG
|||||||||||||||||||||||||||||||||||
MSETEKKIARALFNHIDKSGLKDSSVEELKKRYGG
-------110-------120-------130-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	135	0	0	100.0

Content subtype: combined_34200_6ez4.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1646		99.3 (chain: A, length: 135)
1	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	4692 (1)	noe	98.5 (chain: A, length: 135)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_5	OK	230 (230)	.	95.6 (chain: A, length: 135)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 135, Sequence coverage: 99.3%
- Total number of assignments
  - ¹H chemical shifts: 889
  - ¹³C chemical shifts: 615
  - ¹⁵N chemical shifts: 142
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
569	TYR	HH	11.426
578	TYR	HH	8.914
602	TYR	HH	9.525
619	SER	HG	6.083
663	TYR	HH	9.253

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	900	884	98.2
¹³C chemical shifts	666	615	92.3
¹⁵N chemical shifts	143	142	99.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	265	262	98.9
¹³C chemical shifts	270	267	98.9
¹⁵N chemical shifts	126	125	99.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	635	622	98.0
¹³C chemical shifts	396	348	87.9
¹⁵N chemical shifts	17	17	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	76	76	100.0
¹³C chemical shifts	76	76	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	76	65	85.5
¹³C chemical shifts	76	30	39.5

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 135, Sequence coverage: 98.5%
- Total number of restraints: 4664
- Weight of restraints: 1.0 (4664)
- Potential type of restraints: upper-bound-parabolic (4664)
- Range of distance target values: 2.44, 6.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 135, Sequence coverage: 95.6%
- Total number of restraints: 230
- Total number of restraints per polymer type: 230
- Weight of restraints: 1.0 (230)
- Potential type of restraints: square-well-parabolic (230)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords PIH, R2TP, RNA polymerase, RUVBL1, RUVBL2, Rvb1, Rvb2, snoRNP

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (2.119 seconds)

BMRB: 34200

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. RNA polymerase II-associated protein 3, : 1 : 3 : 20 entities Detail

Interaction partners 1. RNA polymerase II-associated protein 3, : 60 interactors Detail

Experiments performed 18 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail