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Found 1 Document (1.336 seconds)

BMRB: 15637

2K05

Structure of SDF1 in complex with the CXCR4 N-terminus containing sulfotyrosines at postitions 7, 12 and 21

Authors

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

Assembly

CXCL12/SDF1-alpha, CXCR4

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

2. CXCR4 (polymer, Thiol state: not present), 40 monomers, 4755.934 × 2 Da Detail

GSMEGISIXT SDNXTEEMGS GDXDSMKEPA FREENANFNK

Total weight

25859.137 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.

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.5 %, Completeness: 89.9 %, Completeness (bb): 93.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.9 % (1135 of 1262)	89.5 % (598 of 668)	90.4 % (431 of 477)	90.6 % (106 of 117)
Backbone	93.0 % (588 of 632)	92.1 % (197 of 214)	93.0 % (294 of 316)	95.1 % (97 of 102)
Sidechain	88.1 % (645 of 732)	88.3 % (401 of 454)	89.4 % (235 of 263)	60.0 % (9 of 15)
Aromatic	73.7 % (56 of 76)	81.6 % (31 of 38)	64.9 % (24 of 37)	100.0 % (1 of 1)
Methyl	98.9 % (89 of 90)	100.0 % (45 of 45)	97.8 % (44 of 45)

1. CXCL12/SDF1-alpha

GMKPVSLSYR CPCRFFESHV ARANVKHLKI LNTPNCACQI VARLKNNNRQ VCIDPKLKWI QEYLEKCLNK

2. CXCR4

GSMEGISIXT SDNXTEEMGS GDXDSMKEPA FREENANFNK

Show sample condition

Sample #1

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 0.338 mM CXCL12 U-15N/13C (dimer concentration), 0.970 mM unlabled CXCR4, 25 mM MES(d13)

#	Name	Isotope labeling	Concentration
1	CXCL12/SDF1-alpha	[U-100% 13C; U-100% 15N]	0.338 mM
2	CXCR4	natural abundance	0.97 mM
3	MES(d13)		25 mM
4	H2O		90 %
5	D2O		10 %

Sample #2

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 1.07 mM CXCR4 U-15N/13C, 0.670 mM CXCL12 unlabeled (dimer concentration), 25 mM MES(d13)

#	Name	Isotope labeling	Concentration
6	CXCR4	[U-100% 13C; U-100% 15N]	1.07 mM
7	CXCL12/SDF1-alpha	natural abundance	0.67 mM
8	MES(d13)		25 mM
9	H2O		90 %
10	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: -0.59 ppm, Outliers: 1 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: -0.59 ppm, Outliers: 1 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: 0.03 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: 2K05, Strand ID: A, B, C, D 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

Entries sharing articles BMRB: 3, Swiss-Prot: 2 entries Detail

  BMRB: 15633 released on 2008-11-05
    Title Structure of a locked SDF1 dimer
  BMRB: 15635 released on 2008-11-05
    Title Structure of SDF1 in complex with the CXCR4 N-terminus containing a sulfotyrosine at postition 21
  BMRB: 15636 released on 2008-11-05
    Title Structure of SDF1 in complex with the CXCR4 N-terminus containing no sulfotyrosines
  Swiss-Prot: P61073 released on 2004-04-26
    Title CXCR4_HUMAN Entity C-X-C chemokine receptor type 4
  Swiss-Prot: P48061 released on 1996-02-01
    Title SDF1_HUMAN Entity Stromal cell-derived factor 1

Related entities 1. CXCL12/SDF1-alpha, : 1 : 30 entities Detail

Related entities 2. CXCR4, : 1 : 5 : 25 entities Detail

Experiments performed 8 experiments Detail

1 3D_15N-separated_NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 0.338 mM CXCL12 U-15N/13C (dimer concentration), 0.970 mM unlabled CXCR4, 25 mM MES(d13)

#	Name	Isotope labeling	Concentration
1	CXCL12/SDF1-alpha	[U-100% 13C; U-100% 15N]	0.338 mM
2	CXCR4	natural abundance	0.97 mM
3	MES(d13)		25 mM
4	H2O		90 %
5	D2O		10 %

2 3D_13C-separated_NOESY

Instrument

Bruker DRX - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CXCL12/SDF1-alpha	[U-100% 13C; U-100% 15N]	0.338 mM
2	CXCR4	natural abundance	0.97 mM
3	MES(d13)		25 mM
4	H2O		90 %
5	D2O		10 %

3 3D_13C-separated_NOESY (AROMATIC)

Instrument

Bruker DRX - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CXCL12/SDF1-alpha	[U-100% 13C; U-100% 15N]	0.338 mM
2	CXCR4	natural abundance	0.97 mM
3	MES(d13)		25 mM
4	H2O		90 %
5	D2O		10 %

4 3D_13C-F1-filtered_13C-F3-separateded_NOESY

Instrument

Bruker DRX - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CXCL12/SDF1-alpha	[U-100% 13C; U-100% 15N]	0.338 mM
2	CXCR4	natural abundance	0.97 mM
3	MES(d13)		25 mM
4	H2O		90 %
5	D2O		10 %

5 3D_15N-separated_NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 1.07 mM CXCR4 U-15N/13C, 0.670 mM CXCL12 unlabeled (dimer concentration), 25 mM MES(d13)

#	Name	Isotope labeling	Concentration
6	CXCR4	[U-100% 13C; U-100% 15N]	1.07 mM
7	CXCL12/SDF1-alpha	natural abundance	0.67 mM
8	MES(d13)		25 mM
9	H2O		90 %
10	D2O		10 %

6 3D_13C-separated_NOESY

Instrument

Bruker DRX - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	CXCR4	[U-100% 13C; U-100% 15N]	1.07 mM
7	CXCL12/SDF1-alpha	natural abundance	0.67 mM
8	MES(d13)		25 mM
9	H2O		90 %
10	D2O		10 %

7 3D_13C-separated_NOESY (AROMATIC)

Instrument

Bruker DRX - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	CXCR4	[U-100% 13C; U-100% 15N]	1.07 mM
7	CXCL12/SDF1-alpha	natural abundance	0.67 mM
8	MES(d13)		25 mM
9	H2O		90 %
10	D2O		10 %

8 3D_13C-F1-filtered_13C-F3-separateded_NOESY

Instrument

Bruker DRX - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	CXCR4	[U-100% 13C; U-100% 15N]	1.07 mM
7	CXCL12/SDF1-alpha	natural abundance	0.67 mM
8	MES(d13)		25 mM
9	H2O		90 %
10	D2O		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15637_2k05.nef
Input source #2: Coordindates	2k05.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	True (see coodinates for details)
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 40.897 ppm	oxidized, CA 55.447, CB 45.228 ppm	2.03
A:11:CYS:SG	A:50:CYS:SG	unknown	oxidized, CA 58.054, CB 43.162 ppm	2.018
A:36:CYS:SG	C:265:CYS:SG	oxidized, CA 58.616, CB 45.705 ppm	unknown	2.046
A:65:CYS:SG	C:236:CYS:SG	oxidized, CA 56.329, CB 45.235 ppm	unknown	2.041
C:209:CYS:SG	C:234:CYS:SG	unknown	unknown	2.01
C:211:CYS:SG	C:250:CYS:SG	unknown	unknown	2.022

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
3:8:ILE:C	3:9:TYS:N	unknown	unknown	n/a
3:9:TYS:C	3:10:THR:N	unknown	unknown	n/a
3:13:ASN:C	3:14:TYS:N	unknown	unknown	n/a
3:14:TYS:C	3:15:THR:N	unknown	unknown	n/a
3:22:ASP:C	3:23:TYS:N	unknown	unknown	n/a
3:23:TYS:C	3:24:ASP:N	unknown	unknown	n/a
4:8:ILE:C	4:9:TYS:N	unknown	unknown	n/a
4:9:TYS:C	4:10:THR:N	unknown	unknown	n/a
4:13:ASN:C	4:14:TYS:N	unknown	unknown	n/a
4:14:TYS:C	4:15:THR:N	unknown	unknown	n/a
4:22:ASP:C	4:23:TYS:N	unknown	unknown	n/a
4:23:TYS:C	4:24:ASP:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	107	TYS	O-SULFO-L-TYROSINE	Assigned chemical shifts, Distance restraints, Coordinates
B	112	TYS	O-SULFO-L-TYROSINE	Assigned chemical shifts, Distance restraints, Coordinates
B	121	TYS	O-SULFO-L-TYROSINE	Assigned chemical shifts, Distance restraints, Coordinates
D	307	TYS	O-SULFO-L-TYROSINE	Distance restraints, Coordinates
D	312	TYS	O-SULFO-L-TYROSINE	Distance restraints, Coordinates
D	321	TYS	O-SULFO-L-TYROSINE	Distance restraints, Coordinates

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): B vs Auth_asym_ID (model): B

-100-----110-------120-------130--------
GSMEGISIXTSDNXTEEMGSGDXDSMKEPAFREENANFNK
||||||||||||||||||||||||||||||||||||||||
GSMEGISIXTSDNXTEEMGSGDXDSMKEPAFREENANFNK
--------10--------20--------30--------40

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

-200-----210-------220-------230-------240-------250-------260--------
GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK
--------10--------20--------30--------40--------50--------60--------70

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

-300-----310-------320-------330--------
GSMEGISIXTSDNXTEEMGSGDXDSMKEPAFREENANFNK
||||||||||||||||||||||||||||||||||||||||
GSMEGISIXTSDNXTEEMGSGDXDSMKEPAFREENANFNK
--------10--------20--------30--------40

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	70	100.0
B	B	40	100.0
C	C	70	100.0
D	D	40	100.0

Content subtype: combined_15637_2k05.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	18		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1159		94.3 (chain: A, length: 70), 95.0 (chain: B, length: 40)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	2944 (1)	undefined	88.6 (chain: A, length: 70), 77.5 (chain: B, length: 40), 88.6 (chain: C, length: 70), 77.5 (chain: D, length: 40)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	128 (128)	.	71.4 (chain: A, length: 70), 71.4 (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%
  - Entity_assembly_ID: B, Chain length: 40, Sequence coverage: 95.0%
- Total number of assignments
  - ¹H chemical shifts: 622
  - ¹³C chemical shifts: 431
  - ¹⁵N chemical shifts: 106
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	461	417	90.5
¹³C chemical shifts	330	290	87.9
¹⁵N chemical shifts	82	70	85.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	137	125	91.2
¹³C chemical shifts	140	123	87.9
¹⁵N chemical shifts	66	61	92.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	324	292	90.1
¹³C chemical shifts	190	167	87.9
¹⁵N chemical shifts	16	9	56.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	38	36	94.7
¹³C chemical shifts	38	34	89.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	26	92.9
¹³C chemical shifts	27	17	63.0
¹⁵N chemical shifts	1	1	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	231	205	88.7
¹³C chemical shifts	162	141	87.0
¹⁵N chemical shifts	44	36	81.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	83	76	91.6
¹³C chemical shifts	80	73	91.2
¹⁵N chemical shifts	39	36	92.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	148	129	87.2
¹³C chemical shifts	82	68	82.9
¹⁵N chemical shifts	5	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	11	8	72.7
¹³C chemical shifts	11	8	72.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	21	95.5
¹³C chemical shifts	16	11	68.8

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: 88.6%
  - Entity_assembly_ID: B, Chain length: 40, Sequence coverage: 77.5%
  - Entity_assembly_ID: C, Chain length: 70, Sequence coverage: 88.6%
  - Entity_assembly_ID: D, Chain length: 40, Sequence coverage: 77.5%
- Total number of restraints: 2940
- Weight of restraints: 1.0 (2940)
- Potential type of restraints: upper-bound-parabolic (2940)
- 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: B
  - Chain_ID: C
  - Chain_ID: D
- 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: 71.4%
  - Entity_assembly_ID: C, Chain length: 70, Sequence coverage: 71.4%
- Total number of restraints: 128
- Total number of restraints per polymer type: 128
- Weight of restraints: 1.0 (128)
- Potential type of restraints: square-well-parabolic (128)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: C

Keywords chemokine, CXCL12, CXCR4, locked dimer, SDF1-alpha, stromal cell derived factor-1, sulfotyrosine

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Found 1 Document (1.336 seconds)

BMRB: 15637

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 3, Swiss-Prot: 2 entries Detail

Related entities 1. CXCL12/SDF1-alpha, : 1 : 30 entities Detail

Related entities 2. CXCR4, : 1 : 5 : 25 entities Detail

Experiments performed 8 experiments Detail

Instrument

Sample

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NMR combined restraints 4 contents Detail