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Found 1 Document (0.967 seconds)

BMRB: 19354

2MAH

Solution structure of Smoothened

Authors

Rana, R., Lee, H., Zheng, J.J.

Assembly

Smoothened

Entity

1. Smoothened (polymer, Thiol state: all disulfide bound), 128 monomers, 14861.12 Da Detail

SGLVPRGSHM VRRARCYPTS NATNTCFGSK LPYELSSLDL TDFHTEKELN DKLNDYYALK HVPKCWAAIQ PFLCAVFKPK CEKINGEDMV YLPSYEMCRI TMEPCRILYN TTFFPKFLRC NETLFPTK

Formula weight

14861.12 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS16:SG	1:CYS81:SG
2	disulfide	sing	1:CYS26:SG	1:CYS74:SG
3	disulfide	sing	1:CYS65:SG	1:CYS105:SG
4	disulfide	sing	1:CYS98:SG	1:CYS120:SG

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.0 %, Completeness (bb): 97.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.0 % (1485 of 1547)	98.4 % (796 of 809)	92.1 % (563 of 611)	99.2 % (126 of 127)
Backbone	97.6 % (730 of 748)	98.8 % (247 of 250)	96.3 % (366 of 380)	99.2 % (117 of 118)
Sidechain	95.2 % (879 of 923)	98.2 % (549 of 559)	90.4 % (321 of 355)	100.0 % (9 of 9)
Aromatic	78.8 % (126 of 160)	96.2 % (77 of 80)	60.8 % (48 of 79)	100.0 % (1 of 1)
Methyl	97.5 % (117 of 120)	100.0 % (60 of 60)	95.0 % (57 of 60)

1. entity

SGLVPRGSHM VRRARCYPTS NATNTCFGSK LPYELSSLDL TDFHTEKELN DKLNDYYALK HVPKCWAAIQ PFLCAVFKPK CEKINGEDMV YLPSYEMCRI TMEPCRILYN TTFFPKFLRC NETLFPTK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Concentration
1	entity	natural abundance	200 mM
2	acetic acid	[U-2H]	10 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.101329

Referencing offset: -0.08 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.101329

Referencing offset: -0.08 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.101329

Referencing offset: 0.1 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.101329

Referencing offset: -0.01 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MAH, Strand ID: A Detail

Release date

2014-02-12

Citation

Structural insights into the role of the Smoothened cysteine-rich domain in Hedgehog signalling
Rana, R., Carroll, C.E., Lee, H., Bao, J., Marada, S., Grace, C.R.R., Guibao, C.D., Ogden, S.K., Zheng, J.J.
Nat. Commun. (2013), 4, 2965-2965, PubMed 24351982 , DOI 10.1038/ncomms3965 , Abstract

Related entities 1. Smoothened, : 1 : 2 : 25 entities Detail

Interaction partners 1. Smoothened, : 10 interactors Detail

More details for 10 interactors identified by 6 citations

Experiments performed 7 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19354_2mah.nef
Input source #2: Coordindates	2mah.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:27:CYS:SG	A:92:CYS:SG	oxidized, CA 51.785, CB 38.246 ppm	oxidized, CA 53.804, CB 41.219 ppm	1.989
A:37:CYS:SG	A:85:CYS:SG	oxidized, CA 55.634, CB 45.854 ppm	oxidized, CA 57.678, CB 39.396 ppm	1.978
A:76:CYS:SG	A:116:CYS:SG	oxidized, CA 58.297, CB 38.803 ppm	oxidized, CA 54.06, CB 42.879 ppm	1.97
A:109:CYS:SG	A:131:CYS:SG	oxidized, CA 58.737, CB 35.006 ppm	oxidized, CA 54.449, CB 34.958 ppm	1.915

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

-------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-
SGLVPRGSHMVRRARCYPTSNATNTCFGSKLPYELSSLDLTDFHTEKELNDKLNDYYALKHVPKCWAAIQPFLCAVFKPKCEKINGEDMVYLPSYEMCRI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SGLVPRGSHMVRRARCYPTSNATNTCFGSKLPYELSSLDLTDFHTEKELNDKLNDYYALKHVPKCWAAIQPFLCAVFKPKCEKINGEDMVYLPSYEMCRI
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

------120-------130---------
TMEPCRILYNTTFFPKFLRCNETLFPTK
||||||||||||||||||||||||||||
TMEPCRILYNTTFFPKFLRCNETLFPTK
-------110-------120--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	128	0	0	100.0

Content subtype: combined_19354_2mah.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	1479		100.0 (chain: A, length: 128)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1785 (1)	noe	98.4 (chain: A, length: 128)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	139 (139)	.	82.8 (chain: A, length: 128)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 798
  - ¹³C chemical shifts: 556
  - ¹⁵N chemical shifts: 125
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	809	797	98.5
¹³C chemical shifts	611	556	91.0
¹⁵N chemical shifts	134	125	93.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	250	247	98.8
¹³C chemical shifts	256	237	92.6
¹⁵N chemical shifts	118	116	98.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	559	550	98.4
¹³C chemical shifts	355	319	89.9
¹⁵N chemical shifts	16	9	56.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	64	64	100.0
¹³C chemical shifts	64	61	95.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	80	77	96.3
¹³C chemical shifts	79	46	58.2
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 98.4%
- Total number of restraints: 1784
- Weight of restraints: 1.0 (1784)
- Potential type of restraints: upper-bound-parabolic (1784)
- Range of distance target values: 2.49, 5.67 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 82.8%
- Total number of restraints: 139
- Total number of restraints per polymer type: 139
- Weight of restraints: 1.0 (139)
- Potential type of restraints: square-well-parabolic (139)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Hedgehog, Smoothened

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Found 1 Document (0.967 seconds)

BMRB: 19354

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Smoothened, : 1 : 2 : 25 entities Detail

Interaction partners 1. Smoothened, : 10 interactors Detail

Experiments performed 7 experiments Detail

Instrument

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NMR combined restraints 4 contents Detail