BMRBj - BMREntryMaster

Found 1 Document (1.287 seconds)

BMRB: 4981

1G4F

Identification of the phospholipid binding site of human beta2-glycoprotein I domain V by heteronuclear magnetic resonance

Authors

Hoshino, M., Hagihara, Y., Nishii, I., Yamazaki, T., Kato, H., Goto, Y.

Assembly

fifth domain of beta2-glycoprotein I

Entity

1. fifth domain of beta2-glycoprotein I (polymer, Thiol state: all disulfide bound), 86 monomers, 9736.203 Da Detail

TKASCKLPVK KATVVYQGER VKIQEKFKNG MLHGDKVSFF CKNKEKKCSY TEDAQCIDGT IEVPKCFKEH SSLAFWKTDA SDVKPC

Formula weight

9736.203 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	0:CYS5:SG	1:CYS56:SG
2	disulfide	sing	0:CYS41:SG	1:CYS66:SG
3	disulfide	sing	0:CYS48:SG	1:CYS86:SG

Source organism

Homo sapiens

Exptl. method

NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.2 %, Completeness (bb): 97.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.2 % (1004 of 1033)	97.6 % (531 of 544)	96.2 % (385 of 400)	98.9 % (88 of 89)
Backbone	97.8 % (499 of 510)	98.8 % (171 of 173)	96.9 % (246 of 254)	98.8 % (82 of 83)
Sidechain	97.0 % (587 of 605)	97.0 % (360 of 371)	96.9 % (221 of 228)	100.0 % (6 of 6)
Aromatic	95.3 % (82 of 86)	90.7 % (39 of 43)	100.0 % (42 of 42)	100.0 % (1 of 1)
Methyl	100.0 % (72 of 72)	100.0 % (36 of 36)	100.0 % (36 of 36)

1. beta2-glycoprotein I

TKASCKLPVK KATVVYQGER VKIQEKFKNG MLHGDKVSFF CKNKEKKCSY TEDAQCIDGT IEVPKCFKEH SSLAFWKTDA SDVKPC

Show sample condition

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	beta2-glycoprotein I	[U-15N]		1.0 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
2	beta2-glycoprotein I	[U-15N; U-13C]		1.0 mM

LACS Plot; CA

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

Referencing offset: -0.1 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.1 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.01 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.28 ppm, Outliers: 1 Detail

Release date

2001-04-30

Citation 1

Identification of the phospholipid-binding site of human beta(2)-glycoprotein I domain V by heteronuclear magnetic resonance
Hoshino, M., Hagihara, Y., Nishii, I., Yamazaki, T., Kato, H., Goto, Y.
J. Mol. Biol. (2000), 304, 927-939, PubMed 11124037 , DOI 10.1006/jmbi.2000.4243 , Abstract

Show more 2 citaions

Citation 2

NMRPipe: a multidimensional spectral processing system based on UNIX pipes
Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., Bax, A.
J. Biomol. NMR (1995), 6, 277-293, PubMed 8520220 , Abstract

Citation 3

A short recollection on the paper entitled "A common sense approach to peak picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams" by D.S. Garrett, R. Powers, A.M. Gronenborn, and G.M. Clore [J. Magn. Reson. 95 (1991) 214-220]
J. Magn. Reson. (2011), 213, 364-365, PubMed 22152356 , DOI 10.1016/j.jmr.2011.08.009 , Abstract

Hide non-primary 2 citaions

Related entities 1. fifth domain of beta2-glycoprotein I, : 1 : 1 : 3 : 17 entities Detail

Interaction partners 1. fifth domain of beta2-glycoprotein I, : 16 interactors Detail

More details for 16 interactors identified by 8 citations

Experiments performed 7 experiments Detail

1 HNCACB

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker DRX (800 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	beta2-glycoprotein I	[U-15N]		1.0 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
2	beta2-glycoprotein I	[U-15N; U-13C]		1.0 mM

2 CBCA(CO)NH

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker DRX (800 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	beta2-glycoprotein I	[U-15N]		1.0 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
2	beta2-glycoprotein I	[U-15N; U-13C]		1.0 mM

3 HN(CO)CAHA

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker DRX (800 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	beta2-glycoprotein I	[U-15N]		1.0 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
2	beta2-glycoprotein I	[U-15N; U-13C]		1.0 mM

4 1H-13C-1H HCCH-TOCSY

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker DRX (800 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	beta2-glycoprotein I	[U-15N]		1.0 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
2	beta2-glycoprotein I	[U-15N; U-13C]		1.0 mM

5 1H-1H-15N NOESY

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker DRX (800 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	beta2-glycoprotein I	[U-15N]		1.0 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
2	beta2-glycoprotein I	[U-15N; U-13C]		1.0 mM

6 13C-1H-1H NOESY

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker DRX (800 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	beta2-glycoprotein I	[U-15N]		1.0 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
2	beta2-glycoprotein I	[U-15N; U-13C]		1.0 mM

7 HNCO

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker DRX (800 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	beta2-glycoprotein I	[U-15N]		1.0 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
2	beta2-glycoprotein I	[U-15N; U-13C]		1.0 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr4981_3.str
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)
1:5:CYS:SG	1:56:CYS:SG	oxidized, CA 56.78, CB 44.26 ppm	oxidized, CA 55.1, CB 39.12 ppm	n/a
1:41:CYS:SG	1:66:CYS:SG	oxidized, CA 53.04, CB 43.56 ppm	oxidized, CA 56.61, CB 37.29 ppm	n/a
1:48:CYS:SG	1:86:CYS:SG	oxidized, CA 53.76, CB 44.13 ppm	oxidized, CA 56.67, CB 40.75 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr4981_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	shift-1	Warning	1087		100.0 (chain: 1, length: 86)
1	Chemical shift references	chemical_shift_reference	OK	3		No information

Assigned chemical shifts

Saveframe: shift-1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 86, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 610
  - ¹³C chemical shifts: 389
  - ¹⁵N chemical shifts: 88
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
17	GLN	CD	181.19
24	GLN	CD	181.31
29	ASN	CG	178.06
43	ASN	CG	176.4
55	GLN	CD	179.91

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	544	538	98.9
¹³C chemical shifts	400	384	96.0
¹⁵N chemical shifts	90	88	97.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	173	173	100.0
¹³C chemical shifts	172	163	94.8
¹⁵N chemical shifts	83	82	98.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	371	365	98.4
¹³C chemical shifts	228	221	96.9
¹⁵N chemical shifts	7	6	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	37	36	97.3
¹³C chemical shifts	37	36	97.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	43	43	100.0
¹³C chemical shifts	42	42	100.0
¹⁵N chemical shifts	1	1	100.0

Keywords apolipoprotein H, short consensus repeat, complement control protein module, sushi-domain

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Found 1 Document (1.287 seconds)

BMRB: 4981

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. fifth domain of beta2-glycoprotein I, : 1 : 1 : 3 : 17 entities Detail

Interaction partners 1. fifth domain of beta2-glycoprotein I, : 16 interactors Detail

Experiments performed 7 experiments Detail

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Chemical shift validation 3 contents Detail