BMRBj - BMREntryMaster

Found 1 Document (0.979 seconds)

BMRB: 15633

2K01

Structure of a locked SDF1 dimer

Authors

Volkman, B.F., Veldkamp, C.T., Peterson, F.C.

Assembly

CXCL12/SDF1-alpha

Entity

1. CXCL12/SDF1-alpha (polymer, Thiol state: all disulfide bound), 70 monomers, 8173.634 × 2 Da Detail

GMKPVSLSYR CPCRFFESHV ARANVKHLKI LNTPNCACQI VARLKNNNRQ VCIDPKLKWI QEYLEKCLNK

Total weight

16347.268 Da

Max. entity weight

8173.634 Da

Entity Connection

disulfide 6 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS11:SG	1:CYS36:SG
2	disulfide	sing	1:CYS11:SG	1:CYS36:SG
3	disulfide	sing	1:CYS13:SG	1:CYS52:SG
4	disulfide	sing	1:CYS13:SG	1:CYS52:SG
5	disulfide	sing	1:CYS38:SG	1:CYS67:SG
6	disulfide	sing	1:CYS67:SG	1:CYS38: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: 95.7 %, Completeness: 86.1 %, Completeness (bb): 89.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.1 % (747 of 868)	86.3 % (398 of 461)	85.8 % (283 of 330)	85.7 % (66 of 77)
Backbone	89.8 % (370 of 412)	90.5 % (124 of 137)	89.0 % (186 of 209)	90.9 % (60 of 66)
Sidechain	83.8 % (440 of 525)	84.6 % (274 of 324)	84.2 % (160 of 190)	54.5 % (6 of 11)
Aromatic	75.0 % (42 of 56)	89.3 % (25 of 28)	63.0 % (17 of 27)	0.0 % (0 of 1)
Methyl	97.3 % (72 of 74)	97.3 % (36 of 37)	97.3 % (36 of 37)

1. CXCL12/SDF1-alpha

GMKPVSLSYR CPCRFFESHV ARANVKHLKI LNTPNCACQI VARLKNNNRQ VCIDPKLKWI QEYLEKCLNK

Show sample condition

Sample

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.620 mM CXCL12 U-15N/13C (dimer concentration), 25 mM MES(d13)

#	Name	Isotope labeling	Concentration
1	CXCL12/SDF1-alpha	[U-100% 13C; U-100% 15N]	0.620 mM
2	MES(d13)		25 mM
3	H2O		90 %
4	D2O		10 %

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: -0.42 ppm, Outliers: 2 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: -0.42 ppm, Outliers: 2 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: -0.07 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: -0.03 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K01, Strand ID: A, C Detail

Release date

2008-11-05

Citation

Structural basis of CXCR4 sulfotyrosine recognition by the chemokine SDF-1/CXCL12
Veldkamp, C.T., Seibert, C., Peterson, F.C., De la Cruz, N.B., Haugner, J.C., Basnet, H., Sakmar, T.P., Volkman, B.F.
Sci. Signal. (2008), 1, ra4-ra4, PubMed 18799424 , DOI 10.1126/scisignal.1160755 , Abstract

Related entities 1. CXCL12/SDF1-alpha, : 1 : 3 : 23 : 97 entities Detail

Interaction partners 1. CXCL12/SDF1-alpha, : 27 interactors Detail

More details for 27 interactors identified by 5 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_15633_2k01.nef
Input source #2: Coordindates	2k01.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:9:CYS:SG	A:34:CYS:SG	oxidized, CA 53.192, CB 40.25 ppm	oxidized, CA 55.139, CB 45.2 ppm	2.038
A:11:CYS:SG	A:50:CYS:SG	unknown	oxidized, CA 57.984, CB 42.661 ppm	2.008
A:36:CYS:SG	C:265:CYS:SG	oxidized, CA 58.487, CB 45.702 ppm	unknown	2.037
A:65:CYS:SG	C:236:CYS:SG	oxidized, CA 56.102, CB 45.325 ppm	unknown	2.031
C:209:CYS:SG	C:234:CYS:SG	unknown	unknown	2.037
C:211:CYS:SG	C:250:CYS:SG	unknown	unknown	2.007

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

-0--------10--------20--------30--------40--------50--------60--------
GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK
--------10--------20--------30--------40--------50--------60--------70

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	70	0	0	100.0
C	C	70	0	0	100.0

Content subtype: combined_15633_2k01.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	6		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	739		94.3 (chain: A, length: 70)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	3126 (1)	undefined	85.7 (chain: A, length: 70), 85.7 (chain: C, length: 70)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	138 (138)	.	77.1 (chain: A, length: 70), 77.1 (chain: C, length: 70)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 70, Sequence coverage: 94.3%
- Total number of assignments
  - ¹H chemical shifts: 396
  - ¹⁵N chemical shifts: 66
  - ¹³C chemical shifts: 277
- 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	461	396	85.9
¹⁵N chemical shifts	82	66	80.5
¹³C chemical shifts	330	277	83.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	137	122	89.1
¹⁵N chemical shifts	66	60	90.9
¹³C chemical shifts	140	119	85.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	324	274	84.6
¹⁵N chemical shifts	16	6	37.5
¹³C chemical shifts	190	158	83.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	38	36	94.7
¹³C chemical shifts	38	36	94.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	25	89.3
¹⁵N chemical shifts	1	0	0.0
¹³C chemical shifts	27	17	63.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 70, Sequence coverage: 85.7%
  - Entity_assembly_ID: C, Chain length: 70, Sequence coverage: 85.7%
- Total number of restraints: 3120
- Weight of restraints: 1.0 (3120)
- Potential type of restraints: upper-bound-parabolic (3120)
- Range of distance target values: 2.0, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: C
- 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: 70, Sequence coverage: 77.1%
  - Entity_assembly_ID: C, Chain length: 70, Sequence coverage: 77.1%
- Total number of restraints: 138
- Total number of restraints per polymer type: 138
- Weight of restraints: 1.0 (138)
- Potential type of restraints: square-well-parabolic (138)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: C

Keywords chemokine, CXCL12, locked dimer, SDF1-alpha, stromal cell derived factor-1, sulfotyrosine

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Found 1 Document (0.979 seconds)

BMRB: 15633

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. CXCL12/SDF1-alpha, : 1 : 3 : 23 : 97 entities Detail

Interaction partners 1. CXCL12/SDF1-alpha, : 27 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail