BMRBj - BMREntryMaster

Found 1 Document (2.136 seconds)

BMRB: 18082

2LLO

SOLUTION NMR-DERIVED STRUCTURE OF CALMODULIN N-LOBE BOUND WITH ER alpha PEPTIDE

Authors

Zhang, Y.

Assembly

Calmodulin N-lobe bound with ER alpha peptide

Entity

1. Calmodulin N-Lobe (polymer, Thiol state: not present), 80 monomers, 8907.750 Da Detail

ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN GTIDFPEFLT MMARKMKDTD

2. ER alpha peptide (polymer, Thiol state: not present), 19 monomers, 2197.604 Da Detail

RAANLWPSPL MIKRSKKNS

3. CALCIUM ION (non-polymer), 40.078 × 2 Da

Total weight

11185.51 Da

Max. entity weight

8907.75 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: 80.8 %, Completeness: 46.4 %, Completeness (bb): 67.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	46.4 % (529 of 1139)	48.5 % (289 of 596)	37.0 % (162 of 438)	74.3 % (78 of 105)
Backbone	67.9 % (398 of 586)	80.5 % (161 of 200)	54.6 % (159 of 291)	82.1 % (78 of 95)
Sidechain	31.7 % (205 of 646)	32.3 % (128 of 396)	32.1 % (77 of 240)	0.0 % (0 of 10)
Aromatic	0.0 % (0 of 62)	0.0 % (0 of 31)	0.0 % (0 of 30)	0.0 % (0 of 1)
Methyl	13.8 % (13 of 94)	14.9 % (7 of 47)	12.8 % (6 of 47)

1. Calmodulin N-Lobe

ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN GTIDFPEFLT MMARKMKDTD

2. ER alpha peptide

RAANLWPSPL MIKRSKKNS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	Cal_N	[U-100% 13C; U-100% 15N]	1 mM
2	H20	natural abundance	90 %
3	D20	natural abundance	10 %
4	Tris-d11	natural abundance	20 mM
5	sodium chloride	natural abundance	50 mM
6	CaCl2	natural abundance	5 mM

LACS Plot; CA

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

Referencing offset: 0.15 ppm, Outliers: 4 Detail

LACS Plot; CB

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

Referencing offset: 0.15 ppm, Outliers: 4 Detail

LACS Plot; HA

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

Referencing offset: -0.02 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2LLO, Strand ID: A, B Detail

Release date

2015-04-08

Citation

Structural basis for Ca2+-induced activation and dimerization of estrogen receptor α by calmodulin
Zhang, Y., Li, Z., Sacks, D.B., Ames, J.B.
J. Biol. Chem. (2012), 287, 9336-9344, PubMed 22275375 , DOI 10.1074/jbc.M111.334797 , Abstract

Related entities 1. Calmodulin N-Lobe, : 13 : 156 entities Detail

Related entities 2. ER alpha peptide, : 1 : 4 : 13 entities Detail

Interaction partners 2. ER alpha peptide, : 119 interactors Detail

More details for 119 interactors identified by 70 citations

Experiments performed 3 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_18082_2llo.nef
Input source #2: Coordindates	2llo.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)
1:62:THR:O	3:2:CA:CA	unknown	unknown	n/a
1:58:ASP:OD1	3:2:CA:CA	unknown	unknown	n/a
1:24:ASP:OD2	3:1:CA:CA	unknown	unknown	n/a
1:24:ASP:OD1	3:1:CA:CA	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
C	1	CA	CALCIUM ION	None
C	2	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
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTD

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

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	80	0	0	100.0
B	B	19	0	0	100.0

Content subtype: combined_18082_2llo.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_1	Warning	518		100.0 (chain: A, length: 80)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	104 (1)	noe	18.8 (chain: A, length: 80), 100.0 (chain: B, length: 19)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	26 (1)	hbond	94.7 (chain: B, length: 19)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	34 (34)	.	94.7 (chain: B, length: 19)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	34 (34)	.	42.5 (chain: A, length: 80)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 80, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 283
  - ¹³C chemical shifts: 157
  - ¹⁵N chemical shifts: 78
- Completeness of assignments
  - Entity_assemble_ID: A
- 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	466	282	60.5
¹³C chemical shifts	348	157	45.1
¹⁵N chemical shifts	87	78	89.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	164	161	98.2
¹³C chemical shifts	160	80	50.0
¹⁵N chemical shifts	78	78	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	302	121	40.1
¹³C chemical shifts	188	77	41.0
¹⁵N chemical shifts	9	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	6	13.6
¹³C chemical shifts	44	6	13.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	25	0	0.0
¹³C chemical shifts	25	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: 80, Sequence coverage: 18.8%
  - Entity_assembly_ID: B, Chain length: 19, Sequence coverage: 100.0%
- Total number of restraints: 102
- Weight of restraints: 1.0 (102)
- Potential type of restraints: square-well-parabolic (102)
- Range of distance target values: 1.0, 3.5 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: B, Chain length: 19, Sequence coverage: 94.7%
  - Total number of restraints: 26
  - Weight of restraints: 1.0 (26)
  - Potential type of restraints: square-well-parabolic (26)
  - Range of distance target values: 1.15, 1.65 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
      None
    - Chain_ID: B
    - Chain_ID: C
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 19, Sequence coverage: 94.7%
- Total number of restraints: 34
- Total number of restraints per polymer type: 34
- Weight of restraints: 1.0 (34)
- Potential type of restraints: square-well-parabolic (34)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: B

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 80, Sequence coverage: 42.5%
- Total number of restraints: 34
- Potential type of restraints: undefined (34)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

Keywords PROTEIN/PEPTIDE

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Found 1 Document (2.136 seconds)

BMRB: 18082

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Calmodulin N-Lobe, : 13 : 156 entities Detail

Related entities 2. ER alpha peptide, : 1 : 4 : 13 entities Detail

Interaction partners 2. ER alpha peptide, : 119 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail