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Found 1 Document (1.004 seconds)

BMRB: 18170

2LNL

Structure of human CXCR1 in phospholipid bilayers

Authors

Park, S., Das, B.B., Casagrande, F., Nothnagel, H., Chu, M., Kiefer, H., Maier, K., De Angelis, A., Marassi, F.M., Opella, S.J.

Assembly

human CXCR1 in phospholipid bilayers

Entity

1. human CXCR1 in phospholipid bilayers, entity 1 (polymer, Thiol state: free and disulfide bound), 309 monomers, 35124.68 Da Detail

MPPADEDYSP CMLETETLNK YVVIIAYALV FLLSLLGNSL VMLVILYSRV GRSVTDVYLL NLALADLLFA LTLPIWAASK VNGWIFGTFL CKVVSLLKEV NFYSGILLLA CISVDRYLAI VHATRTLTQK RHLVKFVCLG CWGLSMNLSL PFFLFRQAYH PNNSSPVCYE VLGNDTAKWR MVLRILPHTF GFIVPLFVML FCYGFTLRTL FKAHMGQKHR AMRVIFAVVL IFLLCWLPYN LVLLADTLMR TQVIQESCER RNNIGRALDA TEILGFLHSC LNPIIYAFIG QNFRHGFLKI LAMHGLVSK

2. 4-(trifluoromethyl)aniline (non-polymer), 1 monomers, 161.124 Da

Total weight

35285.805 Da

Max. entity weight

35124.68 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS11:SG	1:CYS258:SG
2	disulfide	sing	1:CYS91:SG	1:CYS168:SG

Source organism

Homo sapiens

Exptl. method

NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.4 %, Completeness: 64.1 %, Completeness (bb): 92.6 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	64.1 % (1179 of 1839)	58.2 % (882 of 1516)	92.0 % (297 of 323)
Backbone	92.6 % (1119 of 1209)	90.6 % (825 of 911)	98.7 % (294 of 298)
Sidechain	32.4 % (299 of 923)	33.0 % (296 of 898)	12.0 % (3 of 25)
Aromatic	2.5 % (5 of 201)	2.6 % (5 of 196)	0.0 % (0 of 5)
Methyl	20.8 % (49 of 236)	20.8 % (49 of 236)

1. entity 1

Show sample condition

Sample

Solvent system 100% H2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Concentration
1	CXCR1	[U-100% 13C; U-100% 15N]	2.0 ~ 4.0 mg
2	H2O	natural abundance	100 %
3	HEPES	natural abundance	20 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	solid CH	0.0 ppm	external	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	0.0 ppm	external	direct	1.0

Referencing offset: 0.01 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	solid CH	0.0 ppm	external	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	0.0 ppm	external	direct	1.0

Referencing offset: 0.01 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	solid CH	0.0 ppm	external	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	0.0 ppm	external	direct	1.0

Referencing offset: 0.1 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2012-10-14

Citation

Structure of the chemokine receptor CXCR1 in phospholipid bilayers
Park, S., Das, B.B., Casagrande, F., Tian, Y., Nothnagel, H.J., Chu, M., Kiefer, H., Maier, K., De Angelis, A.A., Marassi, F.M., Opella, S.J.
Nature (2012), 491, 779-783, PubMed 23086146 , DOI 10.1038/nature11580 , Abstract

Related entities 1. human CXCR1 in phospholipid bilayers, entity 1, : 1 : 3 : 1 : 288 entities Detail

Interaction partners 1. human CXCR1 in phospholipid bilayers, entity 1, : 4 interactors Detail

More details for 4 interactors identified by 1 citations

Experiments performed 3 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Dihedral angle restraints, RDC restraints	combined_18170_2lnl.nef
Input source #2: Coordindates	2lnl.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:30:CYS:SG	A:277:CYS:SG	oxidized, CA 56.0, CB 40.3 ppm	oxidized, CA 55.3, CB 39.7 ppm	2.03
A:110:CYS:SG	A:187:CYS:SG	oxidized, CA 55.7, CB 39.4 ppm	oxidized, CA 56.0, CB 40.0 ppm	2.031

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-------12
MPPADEDYSPCMLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALADLLFALTLPIWAASKVNGWIFGTFLCKVVSLLKEV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MPPADEDYSPCMLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALADLLFALTLPIWAASKVNGWIFGTFLCKVVSLLKEV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0-------130-------140-------150-------160-------170-------180-------190-------200-------210-------22
NFYSGILLLACISVDRYLAIVHATRTLTQKRHLVKFVCLGCWGLSMNLSLPFFLFRQAYHPNNSSPVCYEVLGNDTAKWRMVLRILPHTFGFIVPLFVML
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NFYSGILLLACISVDRYLAIVHATRTLTQKRHLVKFVCLGCWGLSMNLSLPFFLFRQAYHPNNSSPVCYEVLGNDTAKWRMVLRILPHTFGFIVPLFVML
-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200

0-------230-------240-------250-------260-------270-------280-------290-------300-------310-------32
FCYGFTLRTLFKAHMGQKHRAMRVIFAVVLIFLLCWLPYNLVLLADTLMRTQVIQESCERRNNIGRALDATEILGFLHSCLNPIIYAFIGQNFRHGFLKI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
FCYGFTLRTLFKAHMGQKHRAMRVIFAVVLIFLLCWLPYNLVLLADTLMRTQVIQESCERRNNIGRALDATEILGFLHSCLNPIIYAFIGQNFRHGFLKI
-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300

0--------
LAMHGLVSK
|||||||||
LAMHGLVSK
---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	309	0	0	100.0

Content subtype: combined_18170_2lnl.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1114		97.4 (chain: A, length: 309)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	590 (590)	.	95.8 (chain: A, length: 309)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_3	OK	267 (267)	.	86.4 (chain: A, length: 309)
2	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	103 (103)	.	33.3 (chain: A, length: 309)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 309, Sequence coverage: 97.4%
- Total number of assignments
  - ¹³C chemical shifts: 816
  - ¹⁵N chemical shifts: 298
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
21	PRO	N	145.0
29	PRO	N	133.0
206	PRO	N	138.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	1516	816	53.8
¹⁵N chemical shifts	339	295	87.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	618	588	95.1
¹⁵N chemical shifts	298	295	99.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	898	228	25.4
¹⁵N chemical shifts	41	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	246	21	8.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	196	0	0.0
¹⁵N chemical shifts	5	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 309, Sequence coverage: 95.8%
- Total number of restraints: 590
- Total number of restraints per polymer type: 590
- Weight of restraints: 1.0 (590)
- Potential type of restraints: square-well-parabolic (590)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_3

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 309, Sequence coverage: 86.4%

20-------30--------40--------50--------60--------70--------80--------90-------100-------110-------12
MPPADEDYSPCMLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALADLLFALTLPIWAASKVNGWIFGTFLCKVVSLLKEV
          ||||||||||||||||||||||||||  ||||||| |||| ||  | |||||||||||||||| |||| || ||||||||||||||||||
..........CMLETETLNKYVVIIAYALVFLLSLL..SLVMLVI.YSRV.RS..D.YLLNLALADLLFALTL.IWAA.KV.GWIFGTFLCKVVSLLKEV
20-------30--------40--------50--------60--------70--------80--------90-------100-------110-------12

0-------130-------140-------150-------160-------170-------180-------190-------200-------210-------22
NFYSGILLLACISVDRYLAIVHATRTLTQKRHLVKFVCLGCWGLSMNLSLPFFLFRQAYHPNNSSPVCYEVLGNDTAKWRMVLRILPHTFGFIVPLFVML
|||||||||||||||||||  |||  ||||||| ||| |||||||||||| | |||||||  ||| |||||||||||||||||||| ||||||| |||||
NFYSGILLLACISVDRYLA..HAT..LTQKRHL.KFV.LGCWGLSMNLSL.F.LFRQAYH..NSS.VCYEVLGNDTAKWRMVLRIL.HTFGFIV.LFVML
0-------130-------140-------150-------160-------170-------180-------190-------200-------210-------22

0-------230-------240-------250-------260-------270-------280-------290-------300-------310-------32
FCYGFTLRTLFKAHMGQKHRAMRVIFAVVLIFLLCWLPYNLVLLADTLMRTQVIQESCERRNNIGRALDATEILGFLHSCLNPIIYAFIGQNFRHGFLKI
||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||| |||||||||||||||| |||||||||||| ||| 
FCYGFTLRTLFKAHMGQKHRAMRVIFAVVLIFLLCWL.YNLVLLADTLMRTQVIQESCERRNNIG.ALDATEILGFLHSCLN.IIYAFIGQNFRH.FLK.
0-------230-------240-------250-------260-------270-------280-------290-------300-------310-------32

0--------
LAMHGLVSK
|||||    
LAMHG    
0----

Total number of restraints: 267
Potential type of restraints: undefined (267)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None
Saveframe: CNS/XPLOR_dipolar_coupling_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 309, Sequence coverage: 33.3%
- Total number of restraints: 103
- Potential type of restraints: undefined (103)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

Keywords 7TM, chemokine, GPCR, G protein coupled receptor, membrane protein, phospholipid, signaling, transmembrane

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Found 1 Document (1.004 seconds)

BMRB: 18170

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. human CXCR1 in phospholipid bilayers, entity 1, : 1 : 3 : 1 : 288 entities Detail

Interaction partners 1. human CXCR1 in phospholipid bilayers, entity 1, : 4 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail