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Found 1 Document (0.652 seconds)

BMRB: 34223

6FDP

NMR structure of the second TPR domain of the human RPAP3 protein in complex with HSP90 peptide DTSRMEEVD

Authors

Quinternet, M., Chagot, M.E., Manival, X.

Assembly

RNA polymerase II-associated protein 3, Heat shock protein HSP 90-alpha

Entity

1. RNA polymerase II-associated protein 3, Heat shock protein HSP 90-alpha, entity 1 (polymer), 120 monomers, 13346.10 Da Detail

GPHMQAISEK DRGNGFFKEG KYERAIECYT RGIAADGANA LLPANRAMAY LKIQKYEEAE KDCTQAILLD GSYSKAFARR GTARTFLGKL NEAKQDFETV LLLEPGNKQA VTELSKIKKK

2. RNA polymerase II-associated protein 3, Heat shock protein HSP 90-alpha, entity 2 (polymer, Thiol state: not present), 9 monomers, 1081.112 Da Detail

DTSRMEEVD

Total weight

14427.212 Da

Max. entity weight

13346.1 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 95.9 %, Completeness (bb): 96.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.9 % (1440 of 1501)	98.5 % (777 of 789)	92.0 % (530 of 576)	97.8 % (133 of 136)
Backbone	96.9 % (744 of 768)	98.5 % (261 of 265)	95.5 % (360 of 377)	97.6 % (123 of 126)
Sidechain	95.7 % (815 of 852)	98.5 % (516 of 524)	90.9 % (289 of 318)	100.0 % (10 of 10)
Aromatic	62.8 % (59 of 94)	85.1 % (40 of 47)	40.4 % (19 of 47)
Methyl	100.0 % (126 of 126)	100.0 % (63 of 63)	100.0 % (63 of 63)

1. entity 1

GPHMQAISEK DRGNGFFKEG KYERAIECYT RGIAADGANA LLPANRAMAY LKIQKYEEAE KDCTQAILLD GSYSKAFARR GTARTFLGKL NEAKQDFETV LLLEPGNKQA VTELSKIKKK

2. entity 2

DTSRMEEVD

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.4, Details 1 mM [U-13C; U-15N] RPAP3-TPR2, 1 mM HSP90-pep, 150 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM TCEP, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP90-pep	natural abundance	1 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM
5	TCEP	natural abundance	0.5 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.4, Details 1 mM [U-13C; U-15N] RPAP3-TPR2, 1 mM HSP90-pep, 150 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM TCEP, 100% D2O

#	Name	Isotope labeling	Concentration
6	RPAP3-TPR2	[U-13C; U-15N]	1 mM
7	HSP90-pep	natural abundance	1 mM
8	sodium chloride	natural abundance	150 mM
9	sodium phosphate	natural abundance	10 mM
10	TCEP	natural abundance	0.5 mM

Release date

2018-01-09

Citation

Deep Structural Analysis of RPAP3 and PIH1D1, Two Components of the HSP90 Co-chaperone R2TP Complex
Henri, J., Chagot, M.E., Bourguet, M., Abel, Y., Terral, G., Maurizy, C., Aigueperse, C., Georgescauld, F., Vandermoere, F., Saint-Fort, R., Behm-Ansmant, I., Charpentier, B., Pradet-Balade, B., Verheggen, C., Bertrand, E., Meyer, P., Cianferani, S., Manival, X., Quinternet, M.
Structure (2018), 26, 1196-1209, PubMed 30033218 , DOI 10.1016/j.str.2018.06.002 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 34224 released on 2018-01-09
Title NMR structure of the second TPR domain of the human RPAP3 protein in complex with HSP70 peptide SGPTIEEVD

Related entities 1. RNA polymerase II-associated protein 3, Heat shock protein HSP 90-alpha, entity 1, : 1 : 125 entities Detail

Related entities 2. RNA polymerase II-associated protein 3, Heat shock protein HSP 90-alpha, entity 2, : 1 entities Detail

Experiments performed 15 experiments Detail

1 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.4, Details 1 mM [U-13C; U-15N] RPAP3-TPR2, 1 mM HSP90-pep, 150 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM TCEP, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP90-pep	natural abundance	1 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM
5	TCEP	natural abundance	0.5 mM

2 3D HNCA

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP90-pep	natural abundance	1 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM
5	TCEP	natural abundance	0.5 mM

3 3D HNCO

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP90-pep	natural abundance	1 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM
5	TCEP	natural abundance	0.5 mM

4 3D HNCACB

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP90-pep	natural abundance	1 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM
5	TCEP	natural abundance	0.5 mM

5 3D HNHA

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP90-pep	natural abundance	1 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM
5	TCEP	natural abundance	0.5 mM

6 3D X-halffiltered 1H-13C NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.4, Details 1 mM [U-13C; U-15N] RPAP3-TPR2, 1 mM HSP90-pep, 150 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM TCEP, 100% D2O

#	Name	Isotope labeling	Concentration
6	RPAP3-TPR2	[U-13C; U-15N]	1 mM
7	HSP90-pep	natural abundance	1 mM
8	sodium chloride	natural abundance	150 mM
9	sodium phosphate	natural abundance	10 mM
10	TCEP	natural abundance	0.5 mM

7 3D HCCH-COSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP90-pep	natural abundance	1 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM
5	TCEP	natural abundance	0.5 mM

8 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP90-pep	natural abundance	1 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM
5	TCEP	natural abundance	0.5 mM

9 3D X-half filtered 1H-15N NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP90-pep	natural abundance	1 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM
5	TCEP	natural abundance	0.5 mM

10 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP90-pep	natural abundance	1 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM
5	TCEP	natural abundance	0.5 mM

11 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP90-pep	natural abundance	1 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM
5	TCEP	natural abundance	0.5 mM

12 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP90-pep	natural abundance	1 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM
5	TCEP	natural abundance	0.5 mM

13 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP90-pep	natural abundance	1 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM
5	TCEP	natural abundance	0.5 mM

14 2D double X-half filtered 1H-1H NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	RPAP3-TPR2	[U-13C; U-15N]	1 mM
7	HSP90-pep	natural abundance	1 mM
8	sodium chloride	natural abundance	150 mM
9	sodium phosphate	natural abundance	10 mM
10	TCEP	natural abundance	0.5 mM

15 2D double X-half filtered 1H-1H NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP90-pep	natural abundance	1 mM
3	sodium chloride	natural abundance	150 mM
4	sodium phosphate	natural abundance	10 mM
5	TCEP	natural abundance	0.5 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34223_6fdp.nef
Input source #2: Coordindates	6fdp.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

---280-----290-------300-------310-------320-------330-------340-------350-------360-------370------
GPHMQAISEKDRGNGFFKEGKYERAIECYTRGIAADGANALLPANRAMAYLKIQKYEEAEKDCTQAILLDGSYSKAFARRGTARTFLGKLNEAKQDFETV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPHMQAISEKDRGNGFFKEGKYERAIECYTRGIAADGANALLPANRAMAYLKIQKYEEAEKDCTQAILLDGSYSKAFARRGTARTFLGKLNEAKQDFETV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-380-------390------
LLLEPGNKQAVTELSKIKKK
||||||||||||||||||||
LLLEPGNKQAVTELSKIKKK
-------110-------120

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

----730--
DTSRMEEVD
|||||||||
DTSRMEEVD
---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	120	0	0	100.0
B	B	9	0	0	100.0

Content subtype: combined_34223_6fdp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1458		99.2 (chain: A, length: 120), 100.0 (chain: B, length: 9)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	3442 (1)	noe	99.2 (chain: A, length: 120), 100.0 (chain: B, length: 9)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	197 (197)	.	91.7 (chain: A, length: 120)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 120, Sequence coverage: 99.2%

---280-----290-------300-------310-------320-------330-------340-------350-------360-------370------
GPHMQAISEKDRGNGFFKEGKYERAIECYTRGIAADGANALLPANRAMAYLKIQKYEEAEKDCTQAILLDGSYSKAFARRGTARTFLGKLNEAKQDFETV
 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
.PHMQAISEKDRGNGFFKEGKYERAIECYTRGIAADGANALLPANRAMAYLKIQKYEEAEKDCTQAILLDGSYSKAFARRGTARTFLGKLNEAKQDFETV

-380-------390------
LLLEPGNKQAVTELSKIKKK
||||||||||||||||||||
LLLEPGNKQAVTELSKIKKK

Entity_assembly_ID: B, Chain length: 9, Sequence coverage: 100.0%

----730--
DTSRMEEVD
|||||||||
DTSRMEEVD

Total number of assignments
- ¹H chemical shifts: 790
- ¹³C chemical shifts: 527
- ¹⁵N chemical shifts: 141

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
306	THR	HG1	5.571
307	ARG	HH11	6.851
307	ARG	HH12	6.851
307	ARG	HH21	6.84
307	ARG	HH22	6.84
322	ARG	HH11	6.677
339	CYS	HG	2.991
340	THR	HG1	5.629
356	ARG	HH21	6.553
356	ARG	HH22	6.553
360	ARG	HH21	6.451
360	ARG	HH22	6.451
361	THR	HG1	5.101

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	740	729	98.5
¹³C chemical shifts	540	504	93.3
¹⁵N chemical shifts	134	133	99.3

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	247	244	98.8
¹³C chemical shifts	240	235	97.9
¹⁵N chemical shifts	117	116	99.1

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	493	485	98.4
¹³C chemical shifts	300	269	89.7
¹⁵N chemical shifts	17	17	100.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	62	61	98.4
¹³C chemical shifts	62	61	98.4

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	47	40	85.1
¹³C chemical shifts	47	17	36.2

Entity_assemble_ID: B

Redox state of CYS
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
- Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	48	98.0
¹³C chemical shifts	36	23	63.9
¹⁵N chemical shifts	10	8	80.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	17	94.4
¹³C chemical shifts	18	5	27.8
¹⁵N chemical shifts	9	7	77.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	31	100.0
¹³C chemical shifts	18	18	100.0
¹⁵N chemical shifts	1	1	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0
¹³C chemical shifts	4	4	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 120, Sequence coverage: 99.2%
  - Entity_assembly_ID: B, Chain length: 9, Sequence coverage: 100.0%
- Total number of restraints: 3426
- Weight of restraints: 1.0 (3426)
- Potential type of restraints: upper-bound-parabolic (3426)
- Range of distance target values: 2.44, 6.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 120, Sequence coverage: 91.7%
- Total number of restraints: 197
- Total number of restraints per polymer type: 197
- Weight of restraints: 1.0 (197)
- Potential type of restraints: square-well-parabolic (197)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords TPR HSP RUVBL Polymerase, chaperone

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Found 1 Document (0.652 seconds)

BMRB: 34223

Sample #1

Sample #2

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. RNA polymerase II-associated protein 3, Heat shock protein HSP 90-alpha, entity 1, : 1 : 125 entities Detail

Related entities 2. RNA polymerase II-associated protein 3, Heat shock protein HSP 90-alpha, entity 2, : 1 entities Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 4 contents Detail