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Found 1 Document (1.102 seconds)

BMRB: 34219

6F9A

Solution structure of the MRH domain of Yos9 complexed with alpha3,alpha6-Man5

Authors

Kniss, A., Kazemi, S., Lohr, F., Guntert, P., Dotsch, V.

Assembly

ER quality-control lectin

Entity

1. ER quality-control lectin (polymer, Thiol state: all disulfide bound), 162 monomers, 18311.46 Da Detail

GASNSEKTAL LTKTLNQGVK TIFDKLNERC IFYQAGFWIY EYCPGIEFVQ FHGRVNTKTG EIVNRDESLV YRLGKPKANV EEREFELLYD DVGYYISEII GSGDICDVTG AERMVEIQYV CGGSNSGPST IQWVRETKIC VYEAQVTIPE LCNLELLAKN ED

Formula weight

18311.46 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS30:SG	1:CYS43:SG
2	disulfide	sing	1:CYS106:SG	1:CYS140:SG
3	disulfide	sing	1:CYS121:SG	1:CYS152:SG

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 95.7 %, Completeness: 90.0 %, Completeness (bb): 93.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.0 % (1700 of 1888)	89.5 % (874 of 977)	91.8 % (676 of 736)	85.7 % (150 of 175)
Backbone	93.6 % (902 of 964)	93.4 % (312 of 334)	93.9 % (443 of 472)	93.0 % (147 of 158)
Sidechain	87.7 % (940 of 1072)	87.4 % (562 of 643)	91.0 % (375 of 412)	17.6 % (3 of 17)
Aromatic	85.6 % (137 of 160)	95.0 % (76 of 80)	75.6 % (59 of 78)	100.0 % (2 of 2)
Methyl	96.8 % (180 of 186)	98.9 % (92 of 93)	94.6 % (88 of 93)

1. entity 1

GASNSEKTAL LTKTLNQGVK TIFDKLNERC IFYQAGFWIY EYCPGIEFVQ FHGRVNTKTG EIVNRDESLV YRLGKPKANV EEREFELLYD DVGYYISEII GSGDICDVTG AERMVEIQYV CGGSNSGPST IQWVRETKIC VYEAQVTIPE LCNLELLAKN ED

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.55 mM [U-98% 13C; U-98% 15N] MRH domain of Yos9, 8.25 mM alpha3,alpha6-Man5, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	MRH domain of Yos9	[U-98% 13C; U-98% 15N]		0.55 mM
2	alpha3,alpha6-Man5	natural abundance		8.25 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 1 mM [U-98% 13C; U-98% 15N] MRH domain of Yos9, 15 mM alpha3,alpha6-Man5, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
3	MRH domain of Yos9	[U-98% 13C; U-98% 15N]		1 mM
4	alpha3,alpha6-Man5	natural abundance		15 mM

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: -0.17 ppm, Outliers: 2 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: -0.17 ppm, Outliers: 2 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: -0.06 ppm, Outliers: 1 Detail

LACS Plot; CO

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: 0.32 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6F9A, Strand ID: A Detail

Release date

2019-01-21

Citation

Structural investigation of glycan recognition by the ERAD quality control lectin Yos9
Kniss, A., Kazemi, S., Lohr, F., Berger, M., Rogov, V.V., Guntert, P., Sommer, T., Jarosch, E., Dotsch, V.
J. Biomol. NMR (2018), 72, 1-10, PubMed 30066206 , DOI 10.1007/s10858-018-0201-6 , Abstract

Related entities 1. ER quality-control lectin, : 2 : 24 entities Detail

Interaction partners 1. ER quality-control lectin, : 8 interactors Detail

More details for 8 interactors identified by 4 citations

Experiments performed 14 experiments Detail

1 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 1 mM [U-98% 13C; U-98% 15N] MRH domain of Yos9, 15 mM alpha3,alpha6-Man5, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
3	MRH domain of Yos9	[U-98% 13C; U-98% 15N]		1 mM
4	alpha3,alpha6-Man5	natural abundance		15 mM

2 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.55 mM [U-98% 13C; U-98% 15N] MRH domain of Yos9, 8.25 mM alpha3,alpha6-Man5, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	MRH domain of Yos9	[U-98% 13C; U-98% 15N]		0.55 mM
2	alpha3,alpha6-Man5	natural abundance		8.25 mM

3 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	MRH domain of Yos9	[U-98% 13C; U-98% 15N]		0.55 mM
2	alpha3,alpha6-Man5	natural abundance		8.25 mM

4 2D 1H-15N HSQC

Instrument

Bruker Avance - 950 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	MRH domain of Yos9	[U-98% 13C; U-98% 15N]		0.55 mM
2	alpha3,alpha6-Man5	natural abundance		8.25 mM

5 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 950 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	MRH domain of Yos9	[U-98% 13C; U-98% 15N]		0.55 mM
2	alpha3,alpha6-Man5	natural abundance		8.25 mM

6 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	MRH domain of Yos9	[U-98% 13C; U-98% 15N]		0.55 mM
2	alpha3,alpha6-Man5	natural abundance		8.25 mM

7 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	MRH domain of Yos9	[U-98% 13C; U-98% 15N]		0.55 mM
2	alpha3,alpha6-Man5	natural abundance		8.25 mM

8 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	MRH domain of Yos9	[U-98% 13C; U-98% 15N]		0.55 mM
2	alpha3,alpha6-Man5	natural abundance		8.25 mM

9 3D HN(COCA)CB

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	MRH domain of Yos9	[U-98% 13C; U-98% 15N]		0.55 mM
2	alpha3,alpha6-Man5	natural abundance		8.25 mM

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	MRH domain of Yos9	[U-98% 13C; U-98% 15N]		0.55 mM
2	alpha3,alpha6-Man5	natural abundance		8.25 mM

11 3D 1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	MRH domain of Yos9	[U-98% 13C; U-98% 15N]		0.55 mM
2	alpha3,alpha6-Man5	natural abundance		8.25 mM

12 3D 13C TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	MRH domain of Yos9	[U-98% 13C; U-98% 15N]		0.55 mM
2	alpha3,alpha6-Man5	natural abundance		8.25 mM

13 2D(HB)CB(CGCD)HD

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	MRH domain of Yos9	[U-98% 13C; U-98% 15N]		0.55 mM
2	alpha3,alpha6-Man5	natural abundance		8.25 mM

14 2D (H)CB(CGCC)H TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	MRH domain of Yos9	[U-98% 13C; U-98% 15N]		0.55 mM
2	alpha3,alpha6-Man5	natural abundance		8.25 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34219_6f9a.nef
Input source #2: Coordindates	6f9a.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:117:CYS:SG	A:130:CYS:SG	oxidized, CA 56.52, CB 47.853 ppm	oxidized, CA 52.236, CB 44.093 ppm	2.053
A:193:CYS:SG	A:227:CYS:SG	oxidized, CA 56.134, CB 43.625 ppm	oxidized, CA 56.757, CB 43.735 ppm	2.011
A:208:CYS:SG	A:239:CYS:SG	oxidized, CA 55.84, CB 40.496 ppm	oxidized, CA 55.182, CB 39.632 ppm	2.026

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

--90------100-------110-------120-------130-------140-------150-------160-------170-------180-------
GASNSEKTALLTKTLNQGVKTIFDKLNERCIFYQAGFWIYEYCPGIEFVQFHGRVNTKTGEIVNRDESLVYRLGKPKANVEEREFELLYDDVGYYISEII
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GASNSEKTALLTKTLNQGVKTIFDKLNERCIFYQAGFWIYEYCPGIEFVQFHGRVNTKTGEIVNRDESLVYRLGKPKANVEEREFELLYDDVGYYISEII
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

190-------200-------210-------220-------230-------240---------
GSGDICDVTGAERMVEIQYVCGGSNSGPSTIQWVRETKICVYEAQVTIPELCNLELLAKNED
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSGDICDVTGAERMVEIQYVCGGSNSGPSTIQWVRETKICVYEAQVTIPELCNLELLAKNED
-------110-------120-------130-------140-------150-------160--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	162	0	0	100.0

Content subtype: combined_34219_6f9a.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1705		95.7 (chain: A, length: 162)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	5043 (1)	noe	95.7 (chain: A, length: 162)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	1527 (1527)	.	99.4 (chain: A, length: 162)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 162, Sequence coverage: 95.7%
- Total number of assignments
  - ¹H chemical shifts: 881
  - ¹³C chemical shifts: 676
  - ¹⁵N chemical shifts: 148
- 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	977	881	90.2
¹³C chemical shifts	736	676	91.8
¹⁵N chemical shifts	182	148	81.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	334	313	93.7
¹³C chemical shifts	324	301	92.9
¹⁵N chemical shifts	158	146	92.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	643	568	88.3
¹³C chemical shifts	412	375	91.0
¹⁵N chemical shifts	24	2	8.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	94	93	98.9
¹³C chemical shifts	94	89	94.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	80	76	95.0
¹³C chemical shifts	78	59	75.6
¹⁵N chemical shifts	2	2	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 162, Sequence coverage: 95.7%
- Total number of restraints: 5043
- Weight of restraints: 1.0 (5043)
- Potential type of restraints: upper-bound-parabolic (5043)
- Range of distance target values: 2.34, 6.44 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 162, Sequence coverage: 99.4%
- Total number of restraints: 1527
- Total number of restraints per polymer type: 1527
- Weight of restraints: 1.0 (1527)
- Potential type of restraints: square-well-parabolic (1527)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords MRH domain, beta barrel, lectin, sugar binding protein

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Found 1 Document (1.102 seconds)

BMRB: 34219

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. ER quality-control lectin, : 2 : 24 entities Detail

Interaction partners 1. ER quality-control lectin, : 8 interactors Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 4 contents Detail