BMRBj - BMREntryMaster

	Total	¹H	¹³C	¹⁵N
All	86.4 % (901 of 1043)	90.3 % (494 of 547)	80.2 % (324 of 404)	90.2 % (83 of 92)
Backbone	85.1 % (439 of 516)	98.3 % (171 of 174)	72.3 % (188 of 260)	97.6 % (80 of 82)
Sidechain	89.0 % (544 of 611)	86.6 % (323 of 373)	95.6 % (218 of 228)	30.0 % (3 of 10)
Aromatic	100.0 % (40 of 40)	100.0 % (20 of 20)	100.0 % (18 of 18)	100.0 % (2 of 2)
Methyl	94.9 % (112 of 118)	93.2 % (55 of 59)	96.6 % (57 of 59)

1. entity 1

ILEAHYTNLK CRCSGVISTV VGLNIIDRIQ VTPPGNGCPK TEVVIWTKMK KVICVNPRAK WLQRLLRHVQ SKSLSSTPQA PVSKRRAA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 850 uM U-[15N] CXCL13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CXCL13	[U-15N]		850 uM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 560 uM U-[15N,13C] CXCL13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
2	CXCL13	[U-15N; U-13C]		560 uM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 250 uM U-[15N] CXCL13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	CXCL13	[U-15N]		250 uM

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	0.1013291

Referencing offset: -0.01 ppm, Outliers: 1 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	0.1013291

Referencing offset: -0.01 ppm, Outliers: 1 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	0.1013291

Referencing offset: -0.02 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5L7M, Strand ID: A Detail

Release date

2017-06-06

Citation

Solution structure of CXCL13 and heparan sulfate binding show that GAG binding site and cellular signalling rely on distinct domains
Monneau, Y.R., Luo, L., Sankaranarayanan, N.V., Nagarajan, B., Vives, R.R., Baleux, F., Desai, U.R., Arenzana-Seidedos, F., Lortat-Jacob, H.
Open Biol. (2017), 7, 170133-170133, PubMed 29070611 , DOI 10.1098/rsob.170133 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 30042 released on 2016-06-09
Title Murin CXCL13 solution structure featuring a folded N-terminal domain

Related entities 1. C-X-C motif chemokine 13, : 1 : 3 : 33 entities Detail

Interaction partners 1. C-X-C motif chemokine 13, : 4 interactors Detail

More details for 4 interactors identified by 2 citations

Experiments performed 12 experiments Detail

1 3D HNCA

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 560 uM U-[15N,13C] CXCL13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
2	CXCL13	[U-15N; U-13C]		560 uM

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 560 uM U-[15N,13C] CXCL13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
2	CXCL13	[U-15N; U-13C]		560 uM

3 2D 1H-13C HSQC aromatic

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 560 uM U-[15N,13C] CXCL13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
2	CXCL13	[U-15N; U-13C]		560 uM

4 3D H(C)CH-TOCSY

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 560 uM U-[15N,13C] CXCL13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
2	CXCL13	[U-15N; U-13C]		560 uM

5 3D (H)CCH-TOCSY

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 560 uM U-[15N,13C] CXCL13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
2	CXCL13	[U-15N; U-13C]		560 uM

6 3D 1H-15N TOCSY-HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 850 uM U-[15N] CXCL13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CXCL13	[U-15N]		850 uM

7 3D 1H-15N NOESY-HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 850 uM U-[15N] CXCL13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CXCL13	[U-15N]		850 uM

8 2D (HB)CB(CG)(CD)HD

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 560 uM U-[15N,13C] CXCL13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
2	CXCL13	[U-15N; U-13C]		560 uM

9 3D 1H-13C NOESY-HMQC

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 560 uM U-[15N,13C] CXCL13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
2	CXCL13	[U-15N; U-13C]		560 uM

10 3D 1H-15N NOESY-HSQC

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 250 uM U-[15N] CXCL13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	CXCL13	[U-15N]		250 uM

11 3D HNCACB

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 560 uM U-[15N,13C] CXCL13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
2	CXCL13	[U-15N; U-13C]		560 uM

12 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 850 uM U-[15N] CXCL13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CXCL13	[U-15N]		850 uM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34005_5l7m.nef
Input source #2: Coordindates	5l7m.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:38:CYS:SG	oxidized, CA 54.826, CB 38.997 ppm	oxidized, CA 52.336, CB 41.831 ppm	2.022
A:13:CYS:SG	A:54:CYS:SG	oxidized, CA 54.667, CB 42.865 ppm	oxidized, CA 57.12, CB 47.633 ppm	2.024

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--------
ILEAHYTNLKCRCSGVISTVVGLNIIDRIQVTPPGNGCPKTEVVIWTKMKKVICVNPRAKWLQRLLRHVQSKSLSSTPQAPVSKRRAA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ILEAHYTNLKCRCSGVISTVVGLNIIDRIQVTPPGNGCPKTEVVIWTKMKKVICVNPRAKWLQRLLRHVQSKSLSSTPQAPVSKRRAA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	88	0	0	100.0

Content subtype: combined_34005_5l7m.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_chemical_shifts_1	Warning	884		98.9 (chain: A, length: 88)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1138 (1)	noe	93.2 (chain: A, length: 88)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	28 (1)	hbond	22.7 (chain: A, length: 88)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	2 (1)	hbond	2.3 (chain: A, length: 88)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	96 (96)	.	67.0 (chain: A, length: 88)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 88, Sequence coverage: 98.9%
- Total number of assignments
  - ¹H chemical shifts: 490
  - ¹³C chemical shifts: 313
  - ¹⁵N chemical shifts: 81
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
47	THR	HG1	5.836

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	547	489	89.4
¹³C chemical shifts	404	313	77.5
¹⁵N chemical shifts	99	81	81.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	174	170	97.7
¹³C chemical shifts	176	95	54.0
¹⁵N chemical shifts	82	79	96.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	373	319	85.5
¹³C chemical shifts	228	218	95.6
¹⁵N chemical shifts	17	2	11.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	56	93.3
¹³C chemical shifts	60	58	96.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	20	100.0
¹³C chemical shifts	18	18	100.0
¹⁵N chemical shifts	2	2	100.0

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: 88, Sequence coverage: 93.2%
- Total number of restraints: 1138
- Weight of restraints: 1.0 (1138)
- Potential type of restraints: square-well-parabolic (1138)
- Range of distance target values: 2.15, 5.47 (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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 88, Sequence coverage: 22.7%
  - Total number of restraints: 28
  - Weight of restraints: 1.0 (28)
  - Potential type of restraints: square-well-parabolic (28)
  - Range of distance target values: 1.98, 2.85 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_4
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 88, Sequence coverage: 2.3%
    - Total number of restraints: 2
    - Weight of restraints: 1.0 (2)
    - Potential type of restraints: square-well-parabolic (2)
    - Range of distance target values: 1.98, 2.85 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 88, Sequence coverage: 67.0%
- Total number of restraints: 96
- Total number of restraints per polymer type: 96
- Weight of restraints: 1.0 (96)
- Potential type of restraints: square-well-parabolic (96)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Chemokine structure, GAG binding, N-terminal domain, Signaling protein

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Found 1 Document (0.743 seconds)

BMRB: 34005

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. C-X-C motif chemokine 13, : 1 : 3 : 33 entities Detail

Interaction partners 1. C-X-C motif chemokine 13, : 4 interactors Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 6 contents Detail