BMRBj - BMREntryMaster

Found 1 Document (1.018 seconds)

BMRB: 15215

2JP1

Solution structure of the alternative conformation of XCL1/Lymphotactin

Authors

Volkman, B.F., Tuinstra, R.L., Peterson, F.C.

Assembly

XCL1/Lymphotactin

Entity

1. XCL1/Lymphotactin (polymer, Thiol state: all disulfide bound), 93 monomers, 10271.66 Da Detail

VGSEVSDKRT CVSLTTQRLP VSRIKTYTIT EGSLRAVIFI TKRGLKVCAD PQATWVRDVV RSMDRKSNTR NNMIQTKPTG TQQSTNTAVT LTG

Formula weight

10271.66 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS11:SG	1:CYS48:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 77.5 %, Completeness (bb): 88.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	77.5 % (816 of 1053)	70.0 % (382 of 546)	85.3 % (347 of 407)	87.0 % (87 of 100)
Backbone	88.2 % (487 of 552)	80.9 % (152 of 188)	91.2 % (250 of 274)	94.4 % (85 of 90)
Sidechain	68.9 % (406 of 589)	64.2 % (230 of 358)	78.7 % (174 of 221)	20.0 % (2 of 10)
Aromatic	76.7 % (23 of 30)	93.3 % (14 of 15)	64.3 % (9 of 14)	0.0 % (0 of 1)
Methyl	79.2 % (95 of 120)	75.0 % (45 of 60)	83.3 % (50 of 60)

1. XCL1

VGSEVSDKRT CVSLTTQRLP VSRIKTYTIT EGSLRAVIFI TKRGLKVCAD PQATWVRDVV RSMDRKSNTR NNMIQTKPTG TQQSTNTAVT LTG

Show sample condition

Sample #1

Solvent system 95% H2O, 5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.0, Details 1.0 mM XCL1 U-15N/13C, 20 mM sodium phosphate

#	Name	Isotope labeling	Type	Concentration
1	XCL1	[U-100% 13C; U-100% 15N]		1.0 mM
2	sodium phosphate	natural abundance		20 mM

Sample #2

Solvent system 95% H2O, 5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.0, Details 0.6 mM XCL1 U-15N/13C, 0.6 mM XCL1 unlabeled, 20 mM sodium phosphate

#	Name	Isotope labeling	Concentration
3	XCL1	[U-100% 13C; U-100% 15N]	0.6 mM
4	XCL1	natural abundance	0.6 mM
5	sodium phosphate	natural abundance	20 mM

LACS Plot; CA

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

Referencing offset: -0.26 ppm, Outliers: 4 Detail

LACS Plot; CB

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

Referencing offset: -0.26 ppm, Outliers: 4 Detail

LACS Plot; HA

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

Referencing offset: -0.12 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.42 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JP1, Strand ID: A, B Detail

Release date

2007-10-28

Citation

An engineered second disulfide bond restricts lymphotactin/XCL1 to a chemokine-like conformation with XCR1 agonist activity
Tuinstra, R.L., Peterson, F.C., Elgin, E.S., Pelzek, A.J., Volkman, B.F.
Biochemistry (2007), 46, 2564-2573, PubMed 17302442 , DOI 10.1021/bi602365d , Abstract

Related entities 1. XCL1/Lymphotactin, : 1 : 5 : 2 : 10 entities Detail

Interaction partners 1. XCL1/Lymphotactin, : 18 interactors Detail

More details for 18 interactors identified by 3 citations

Experiments performed 3 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15215_2jp1.nef
Input source #2: Coordindates	2jp1.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:11:CYS:SG	A:48:CYS:SG	oxidized, CA 55.428, CB 49.956 ppm	oxidized, CA 55.1, CB 48.662 ppm	2.036
B:11:CYS:SG	B:48:CYS:SG	unknown	unknown	2.029

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90---
VGSEVSDKRTCVSLTTQRLPVSRIKTYTITEGSLRAVIFITKRGLKVCADPQATWVRDVVRSMDRKSNTRNNMIQTKPTGTQQSTNTAVTLTG
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
VGSEVSDKRTCVSLTTQRLPVSRIKTYTITEGSLRAVIFITKRGLKVCADPQATWVRDVVRSMDRKSNTRNNMIQTKPTGTQQSTNTAVTLTG

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90---
VGSEVSDKRTCVSLTTQRLPVSRIKTYTITEGSLRAVIFITKRGLKVCADPQATWVRDVVRSMDRKSNTRNNMIQTKPTGTQQSTNTAVTLTG
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
VGSEVSDKRTCVSLTTQRLPVSRIKTYTITEGSLRAVIFITKRGLKVCADPQATWVRDVVRSMDRKSNTRNNMIQTKPTGTQQSTNTAVTLTG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	93	0	0	100.0
B	B	93	0	0	100.0

Content subtype: combined_15215_2jp1.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	802		100.0 (chain: A, length: 93)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	2090 (1)	noe	60.2 (chain: A, length: 93), 60.2 (chain: B, length: 93)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	65 (65)	.	46.2 (chain: A, length: 93)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 373
  - ¹³C chemical shifts: 344
  - ¹⁵N chemical shifts: 85
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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	546	373	68.3
¹³C chemical shifts	407	344	84.5
¹⁵N chemical shifts	109	85	78.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	188	153	81.4
¹³C chemical shifts	186	173	93.0
¹⁵N chemical shifts	90	85	94.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	358	220	61.5
¹³C chemical shifts	221	171	77.4
¹⁵N chemical shifts	19	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	62	44	71.0
¹³C chemical shifts	62	49	79.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	14	93.3
¹³C chemical shifts	14	9	64.3
¹⁵N chemical shifts	1	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 60.2%
  - Entity_assembly_ID: B, Chain length: 93, Sequence coverage: 60.2%
- Total number of restraints: 2077
- Weight of restraints: 1.0 (2077)
- Potential type of restraints: upper-bound-parabolic (2077)
- Range of distance target values: 2.1, 5.5 (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: 93, Sequence coverage: 46.2%
- Total number of restraints: 65
- Total number of restraints per polymer type: 65
- Weight of restraints: 1.0 (65)
- Potential type of restraints: square-well-parabolic (65)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords chemokine, Lymphotactin, protein folding, structural rearrangement, XCL1

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Found 1 Document (1.018 seconds)

BMRB: 15215

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. XCL1/Lymphotactin, : 1 : 5 : 2 : 10 entities Detail

Interaction partners 1. XCL1/Lymphotactin, : 18 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail