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BMRB: 34224

6FDT

NMR structure of the second TPR domain of the human RPAP3 protein in complex with HSP70 peptide SGPTIEEVD

Authors

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

Assembly

RNA polymerase II-associated protein 3, Heat shock 70 kDa protein 1B

Entity

1. RNA polymerase II-associated protein 3, Heat shock 70 kDa protein 1B, 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 70 kDa protein 1B, entity 2 (polymer, Thiol state: not present), 9 monomers, 945.9668 Da Detail

SGPTIEEVD

Total weight

14292.066 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: 100.0 %, Completeness: 93.2 %, Completeness (bb): 94.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.2 % (1395 of 1497)	95.9 % (754 of 786)	88.9 % (512 of 576)	95.6 % (129 of 135)
Backbone	94.3 % (722 of 766)	96.2 % (255 of 265)	92.6 % (348 of 376)	95.2 % (119 of 125)
Sidechain	92.3 % (784 of 849)	95.8 % (499 of 521)	86.5 % (275 of 318)	100.0 % (10 of 10)
Aromatic	58.5 % (55 of 94)	74.5 % (35 of 47)	42.6 % (20 of 47)
Methyl	96.9 % (126 of 130)	100.0 % (65 of 65)	93.8 % (61 of 65)

1. entity 1

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

2. entity 2

SGPTIEEVD

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 HSP70-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	HSP70-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 HSP70-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	HSP70-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

Related entities 1. RNA polymerase II-associated protein 3, Heat shock 70 kDa protein 1B, entity 1, : 1 : 125 entities Detail

Experiments performed 16 experiments Detail

1 3D HNCA

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 HSP70-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	HSP70-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 HNCACB

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP70-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 CBCA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP70-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 HNCO

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP70-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	HSP70-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 2D double X-half filtered 1H-1H 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 HSP70-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	HSP70-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 X-half filtered 1H-13C NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	RPAP3-TPR2	[U-13C; U-15N]	1 mM
7	HSP70-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

8 3D X-half filtered 1H-13C NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP70-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	HSP70-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 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP70-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 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP70-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 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP70-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 HCCH-TOCSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP70-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 1H-15N HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP70-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

15 3D HCCH-COSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RPAP3-TPR2	[U-13C; U-15N]	1 mM
2	HSP70-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

16 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	RPAP3-TPR2	[U-13C; U-15N]	1 mM
7	HSP70-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

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34224_6fdt.nef
Input source #2: Coordindates	6fdt.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

--640----
SGPTIEEVD
|||||||||
SGPTIEEVD
---------

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_34224_6fdt.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1432		99.2 (chain: A, length: 120), 100.0 (chain: B, length: 9)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	4062 (1)	noe	99.2 (chain: A, length: 120), 88.9 (chain: B, length: 9)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	199 (199)	.	93.3 (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%

--640----
SGPTIEEVD
|||||||||
SGPTIEEVD

Total number of assignments
- ¹H chemical shifts: 792
- ¹³C chemical shifts: 508
- ¹⁵N chemical shifts: 132

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
300	ARG	HH11	7.237
300	ARG	HH12	7.237
304	CYS	HG	2.837
306	THR	HG1	5.594
307	ARG	HH11	6.795
307	ARG	HH12	6.795
307	ARG	HH21	6.809
307	ARG	HH22	6.809
322	ARG	HH11	6.674
322	ARG	HH12	6.674
339	CYS	HG	2.987
340	THR	HG1	5.613
356	ARG	HH11	6.551
356	ARG	HH12	6.551
356	ARG	HH21	6.714
356	ARG	HH22	6.714
360	ARG	HH21	6.455
360	ARG	HH22	6.455
361	THR	HG1	5.138

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	740	728	98.4
¹³C chemical shifts	540	508	94.1
¹⁵N chemical shifts	134	132	98.5

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	484	98.2
¹³C chemical shifts	300	273	91.0
¹⁵N chemical shifts	17	16	94.1

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	62	62	100.0
¹³C chemical shifts	62	62	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	47	39	83.0
¹³C chemical shifts	47	20	42.6

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	46	45	97.8
¹³C chemical shifts	36	0	0.0
¹⁵N chemical shifts	8	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	17	94.4
¹³C chemical shifts	18	0	0.0
¹⁵N chemical shifts	8	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	28	100.0
¹³C chemical shifts	18	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	100.0
¹³C chemical shifts	5	0	0.0

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: 88.9%
- Total number of restraints: 4056
- Weight of restraints: 1.0 (4056)
- Potential type of restraints: upper-bound-parabolic (4056)
- Range of distance target values: 2.4, 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: 93.3%
- Total number of restraints: 199
- Total number of restraints per polymer type: 199
- Weight of restraints: 1.0 (199)
- Potential type of restraints: square-well-parabolic (199)
- 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 (0.931 seconds)

BMRB: 34224

Sample #1

Sample #2

Related entities 1. RNA polymerase II-associated protein 3, Heat shock 70 kDa protein 1B, entity 1, : 1 : 125 entities Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 4 contents Detail