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Found 1 Document (0.722 seconds)

BMRB: 19960

2MP1

Solution structure of the human chemokine CCL19

Authors

Veldkamp, C.T., Peterson, F.C., Gabel-Eissens, S.J., Gillitzer, M.L.

Assembly

Human Chemokine CCL19

Entity

1. Human Chemokine CCL19 (polymer, Thiol state: all disulfide bound), 77 monomers, 8800.167 Da Detail

GTNDAEDCCL SVTQKPIPGY IVRNFHYLLI KDGCRVPAVV FTTLRGRQLC APPDQPWVER IIQRLQRTSA KMKRRSS

Formula weight

8800.167 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS8:SG	1:CYS34:SG
2	disulfide	sing	1:CYS9:SG	1:CYS50: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, 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: 87.5 %, Completeness (bb): 80.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.5 % (801 of 915)	95.4 % (461 of 483)	74.5 % (263 of 353)	97.5 % (77 of 79)
Backbone	80.9 % (364 of 450)	96.7 % (147 of 152)	65.2 % (148 of 227)	97.2 % (69 of 71)
Sidechain	94.6 % (509 of 538)	94.9 % (314 of 331)	94.0 % (187 of 199)	100.0 % (8 of 8)
Aromatic	84.6 % (44 of 52)	100.0 % (26 of 26)	68.0 % (17 of 25)	100.0 % (1 of 1)
Methyl	96.5 % (83 of 86)	95.3 % (41 of 43)	97.7 % (42 of 43)

1. Human Chemokine CCL19

GTNDAEDCCL SVTQKPIPGY IVRNFHYLLI KDGCRVPAVV FTTLRGRQLC APPDQPWVER IIQRLQRTSA KMKRRSS

Show sample condition

Sample

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.6, Details 0.515mM CCL19-U-15N/13C pH 5.6 25mM deuterated MES buffer

#	Name	Isotope labeling	Concentration
1	Human Chemokine CCL19	[U-100% 13C; U-100% 15N]	0.515 mM
2	D2O	[U-99% 2H]	10 %
3	dueterated MES	[U-100% 2H]	25 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: -0.34 ppm, Outliers: 1 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: -0.34 ppm, Outliers: 1 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: -0.11 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MP1, Strand ID: A Detail

Release date

2015-06-07

Citation

Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites
Veldkamp, C.T.., Peterson, F.C., Gabel-Eissens, S.J., Gillitzer, M.L.
Biochemistry (2015), 54, 4163-4166, PubMed 26115234 , DOI 10.1021/acs.biochem.5b00560 , Abstract

Related entities 1. Human Chemokine CCL19, : 1 : 2 : 1 : 237 entities Detail

Interaction partners 1. Human Chemokine CCL19, : 2 interactors Detail

More details for 2 interactors identified by 2 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_19960_2mp1.nef
Input source #2: Coordindates	2mp1.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:8:CYS:SG	A:34:CYS:SG	oxidized, CA 55.968, CB 39.801 ppm	oxidized, CA 52.512, CB 38.017 ppm	2.041
A:9:CYS:SG	A:50:CYS:SG	oxidized, CA 57.64, CB 44.2 ppm	oxidized, CA 57.25, CB 48.72 ppm	2.001

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-------
GTNDAEDCCLSVTQKPIPGYIVRNFHYLLIKDGCRVPAVVFTTLRGRQLCAPPDQPWVERIIQRLQRTSAKMKRRSS
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GTNDAEDCCLSVTQKPIPGYIVRNFHYLLIKDGCRVPAVVFTTLRGRQLCAPPDQPWVERIIQRLQRTSAKMKRRSS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	77	0	0	100.0

Content subtype: combined_19960_2mp1.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	815		100.0 (chain: A, length: 77)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	2851 (1)	noe	100.0 (chain: A, length: 77)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	85 (85)	.	80.5 (chain: A, length: 77)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 77, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 471
  - ¹³C chemical shifts: 267
  - ¹⁵N chemical shifts: 77
- 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	483	471	97.5
¹³C chemical shifts	353	267	75.6
¹⁵N chemical shifts	88	77	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	152	150	98.7
¹³C chemical shifts	154	77	50.0
¹⁵N chemical shifts	71	69	97.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	331	321	97.0
¹³C chemical shifts	199	190	95.5
¹⁵N chemical shifts	17	8	47.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	43	97.7
¹³C chemical shifts	44	43	97.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	26	100.0
¹³C chemical shifts	25	17	68.0
¹⁵N chemical shifts	1	1	100.0

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: 77, Sequence coverage: 100.0%
- Total number of restraints: 2726
- Weight of restraints: 1.0 (2726)
- Potential type of restraints: upper-bound-parabolic (2726)
- 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
- 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: 77, Sequence coverage: 80.5%
- Total number of restraints: 85
- Total number of restraints per polymer type: 85
- Weight of restraints: 1.0 (85)
- Potential type of restraints: square-well-parabolic (85)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords CCL19, CCL21, CCR7, chemokine receptors, chemokines

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Found 1 Document (0.722 seconds)

BMRB: 19960

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Human Chemokine CCL19, : 1 : 2 : 1 : 237 entities Detail

Interaction partners 1. Human Chemokine CCL19, : 2 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail