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Found 1 Document (0.912 seconds)

BMRB: 30156

5T0X

Solution NMR-derived structure of calmodulin bound with ER alpha peptides

Authors

Zhang, Y., Ames, J.B.

Assembly

Calmodulin, Estrogen receptor peptide

Entity

1. Calmodulin (polymer, Thiol state: not present), 148 monomers, 16706.21 Da Detail

ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK

2. Estrogen receptor peptide (polymer, Thiol state: not present), 19 monomers, 2197.604 × 2 Da Detail

RAANLWPSPL MIKRSKKNS

3. CALCIUM ION (non-polymer), 40.078 × 4 Da

Total weight

21261.73 Da

Max. entity weight

16706.21 Da

Source organism

Xenopus laevis , Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 89.2 %, Completeness: 60.0 %, Completeness (bb): 86.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	60.0 % (1146 of 1910)	53.8 % (536 of 997)	63.1 % (464 of 735)	82.0 % (146 of 178)
Backbone	86.1 % (856 of 994)	85.9 % (293 of 341)	85.1 % (417 of 490)	89.6 % (146 of 163)
Sidechain	39.6 % (424 of 1072)	37.0 % (243 of 656)	45.1 % (181 of 401)	0.0 % (0 of 15)
Aromatic	5.4 % (6 of 112)	7.1 % (4 of 56)	3.6 % (2 of 55)	0.0 % (0 of 1)
Methyl	57.0 % (90 of 158)	60.8 % (48 of 79)	53.2 % (42 of 79)

1. Calmodulin

ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK

2. Estrogen receptor peptide

RAANLWPSPL MIKRSKKNS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0, Details 1 mM [U-99% 15N] 15N-labeled CaM/ERalpha, 0.6 mM [U-99% 13C; U-99% 15N] 13C/15N-CaM/ERalpha, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	13C/15N-CaM/ERalpha	[U-99% 13C; U-99% 15N]	0.6 mM
2	15N-labeled CaM/ERalpha	[U-99% 15N]	1 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %
5	Tris-d11	natural abundance	20 mM
6	CaCl2	natural abundance	5 mM
7	NaCl	natural abundance	50 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	internal	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 0.1 ppm, Outliers: 1 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	internal	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 0.1 ppm, Outliers: 1 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	internal	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 0.0 ppm, Outliers: 2 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	internal	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.73 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 5T0X, Strand ID: A, B, C Detail

Release date

2016-11-20

Citation

Solution NMR-derived structure of calmodulin bound with ER alpha peptides
Zhang, Y., Ames, J.B.

Related entities 1. Calmodulin, : 11 : 88 entities Detail

Related entities 2. Estrogen receptor peptide, : 1 : 3 : 2 entities Detail

Experiments performed 5 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker 1 - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0, Details 1 mM [U-99% 15N] 15N-labeled CaM/ERalpha, 0.6 mM [U-99% 13C; U-99% 15N] 13C/15N-CaM/ERalpha, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	13C/15N-CaM/ERalpha	[U-99% 13C; U-99% 15N]	0.6 mM
2	15N-labeled CaM/ERalpha	[U-99% 15N]	1 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %
5	Tris-d11	natural abundance	20 mM
6	CaCl2	natural abundance	5 mM
7	NaCl	natural abundance	50 mM

2 3D HNCO

Instrument

Bruker 1 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	13C/15N-CaM/ERalpha	[U-99% 13C; U-99% 15N]	0.6 mM
2	15N-labeled CaM/ERalpha	[U-99% 15N]	1 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %
5	Tris-d11	natural abundance	20 mM
6	CaCl2	natural abundance	5 mM
7	NaCl	natural abundance	50 mM

3 3D HNCACB

Instrument

Bruker 1 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	13C/15N-CaM/ERalpha	[U-99% 13C; U-99% 15N]	0.6 mM
2	15N-labeled CaM/ERalpha	[U-99% 15N]	1 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %
5	Tris-d11	natural abundance	20 mM
6	CaCl2	natural abundance	5 mM
7	NaCl	natural abundance	50 mM

4 3D CBCA(CO)NH

Instrument

Bruker 1 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	13C/15N-CaM/ERalpha	[U-99% 13C; U-99% 15N]	0.6 mM
2	15N-labeled CaM/ERalpha	[U-99% 15N]	1 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %
5	Tris-d11	natural abundance	20 mM
6	CaCl2	natural abundance	5 mM
7	NaCl	natural abundance	50 mM

5 3D HBHA(CO)NH

Instrument

Bruker 1 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	13C/15N-CaM/ERalpha	[U-99% 13C; U-99% 15N]	0.6 mM
2	15N-labeled CaM/ERalpha	[U-99% 15N]	1 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %
5	Tris-d11	natural abundance	20 mM
6	CaCl2	natural abundance	5 mM
7	NaCl	natural abundance	50 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30156_5t0x.nef
Input source #2: Coordindates	5t0x.cif
Diamagnetism of the molecular assembly	False (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)
1:20:ASP:OD1	4:1:CA:CA	unknown	unknown	n/a
1:20:ASP:OD2	4:1:CA:CA	unknown	unknown	n/a
1:22:ASP:OD1	4:1:CA:CA	unknown	unknown	n/a
1:22:ASP:OD2	4:1:CA:CA	unknown	unknown	n/a
1:24:ASP:OD2	4:1:CA:CA	unknown	unknown	n/a
1:26:THR:O	4:1:CA:CA	unknown	unknown	n/a
1:31:GLU:OE1	4:1:CA:CA	unknown	unknown	n/a
1:56:ASP:OD1	4:2:CA:CA	unknown	unknown	n/a
1:58:ASP:OD1	4:2:CA:CA	unknown	unknown	n/a
1:58:ASP:OD2	4:2:CA:CA	unknown	unknown	n/a
1:60:ASN:OD1	4:2:CA:CA	unknown	unknown	n/a
1:62:THR:O	4:2:CA:CA	unknown	unknown	n/a
1:64:ASP:OD2	4:2:CA:CA	unknown	unknown	n/a
1:67:GLU:OE1	4:2:CA:CA	unknown	unknown	n/a
1:67:GLU:OE2	4:2:CA:CA	unknown	unknown	n/a
1:93:ASP:O	4:3:CA:CA	unknown	unknown	n/a
1:93:ASP:OD1	4:3:CA:CA	unknown	unknown	n/a
1:95:ASP:OD2	4:3:CA:CA	unknown	unknown	n/a
1:97:ASN:OD1	4:3:CA:CA	unknown	unknown	n/a
1:99:TYR:O	4:3:CA:CA	unknown	unknown	n/a
1:104:GLU:OE1	4:3:CA:CA	unknown	unknown	n/a
1:129:ASP:OD1	4:4:CA:CA	unknown	unknown	n/a
1:131:ASP:OD2	4:4:CA:CA	unknown	unknown	n/a
1:133:ASP:OD1	4:4:CA:CA	unknown	unknown	n/a
1:133:ASP:OD2	4:4:CA:CA	unknown	unknown	n/a
1:135:GLN:O	4:4:CA:CA	unknown	unknown	n/a
1:140:GLU:OE1	4:4:CA:CA	unknown	unknown	n/a
1:140:GLU:OE2	4:4:CA:CA	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
D	1	CA	CALCIUM ION	None
D	2	CA	CALCIUM ION	None
D	3	CA	CALCIUM ION	None
D	4	CA	CALCIUM ION	None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI

-------110-------120-------130-------140--------
SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK
||||||||||||||||||||||||||||||||||||||||||||||||
SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

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

---290-----300-----
RAANLWPSPLMIKRSKKNS
|||||||||||||||||||
RAANLWPSPLMIKRSKKNS
--------10---------

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

---290-----300-----
RAANLWPSPLMIKRSKKNS
|||||||||||||||||||
RAANLWPSPLMIKRSKKNS
--------10---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	148	100.0
B	B	19	100.0
C	C	19	100.0

Content subtype: combined_30156_5t0x.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	28		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1088		100.0 (chain: A, length: 148)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	223 (1)	noe	21.6 (chain: A, length: 148), 100.0 (chain: B, length: 19), 100.0 (chain: C, length: 19)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	62 (1)	hbond	6.1 (chain: A, length: 148), 94.7 (chain: B, length: 19), 94.7 (chain: C, length: 19)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	Warning	74 (74)	.	4.7 (chain: A, length: 148), 94.7 (chain: B, length: 19), 94.7 (chain: C, length: 19)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 506
  - ¹³C chemical shifts: 437
  - ¹⁵N chemical shifts: 145
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	867	506	58.4
¹³C chemical shifts	645	437	67.8
¹⁵N chemical shifts	164	145	88.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	305	291	95.4
¹³C chemical shifts	296	276	93.2
¹⁵N chemical shifts	146	145	99.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	562	215	38.3
¹³C chemical shifts	349	161	46.1
¹⁵N chemical shifts	18	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	80	47	58.8
¹³C chemical shifts	80	39	48.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	0	0.0
¹³C chemical shifts	50	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 21.6%
  - Entity_assembly_ID: B, Chain length: 19, Sequence coverage: 100.0%
  - Entity_assembly_ID: C, Chain length: 19, Sequence coverage: 100.0%
- Total number of restraints: 221
- Weight of restraints: 1.0 (221)
- Potential type of restraints: square-well-parabolic (221)
- Range of distance target values: 1.0, 1.25 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D
    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: 148, Sequence coverage: 6.1%
    - Entity_assembly_ID: B, Chain length: 19, Sequence coverage: 94.7%
    - Entity_assembly_ID: C, Chain length: 19, Sequence coverage: 94.7%
  - Total number of restraints: 62
  - Weight of restraints: 1.0 (62)
  - Potential type of restraints: square-well-parabolic (62)
  - Range of distance target values: 1.15, 1.65 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
    - Chain_ID: D
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 4.7%
  - Entity_assembly_ID: B, Chain length: 19, Sequence coverage: 94.7%
  - Entity_assembly_ID: C, Chain length: 19, Sequence coverage: 94.7%
- Total number of restraints: 74
- Total number of restraints per polymer type: 74
- Weight of restraints: 1.0 (74)
- Potential type of restraints: square-well-parabolic (74)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: B
  - Chain_ID: C

Keywords calmodulin, complex, estrogen receptor

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Found 1 Document (0.912 seconds)

BMRB: 30156

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Calmodulin, : 11 : 88 entities Detail

Related entities 2. Estrogen receptor peptide, : 1 : 3 : 2 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail