BMRBj - BMREntryMaster

Found 1 Document (0.766 seconds)

BMRB: 30584

Solution structure of human myeloid-derived growth factor

Authors

Bortnov, V., Tonelli, M., Lee, W., Markley, J.L., Mosher, D.F.

Assembly

Myeloid-derived growth factor

Entity

1. Myeloid-derived growth factor (polymer, Thiol state: all disulfide bound), 147 monomers, 16265.02 Da Detail

GSKGTVSEPT TVAFDVRPGG VVHSFSHNVG PGDKYTCMFT YASQGGTNEQ WQMSLGTSED HQHFTCTIWR PQGKSYLYFT QFKAEVRGAE IEYAMAYSKA AFERESDVPL KTEEFEVTKT AVAHRPGAFK AELSKLVIVA KASRTEL

Formula weight

16265.02 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS37:SG	1:CYS66:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamicsmolecular dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.8 %, Completeness (bb): 98.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.8 % (1622 of 1676)	97.0 % (837 of 863)	96.1 % (636 of 662)	98.7 % (149 of 151)
Backbone	98.6 % (858 of 870)	99.3 % (298 of 300)	98.1 % (421 of 429)	98.6 % (139 of 141)
Sidechain	95.5 % (899 of 941)	95.7 % (539 of 563)	95.1 % (350 of 368)	100.0 % (10 of 10)
Aromatic	83.5 % (152 of 182)	83.5 % (76 of 91)	83.1 % (74 of 89)	100.0 % (2 of 2)
Methyl	100.0 % (140 of 140)	100.0 % (70 of 70)	100.0 % (70 of 70)

1. entity 1

GSKGTVSEPT TVAFDVRPGG VVHSFSHNVG PGDKYTCMFT YASQGGTNEQ WQMSLGTSED HQHFTCTIWR PQGKSYLYFT QFKAEVRGAE IEYAMAYSKA AFERESDVPL KTEEFEVTKT AVAHRPGAFK AELSKLVIVA KASRTEL

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 8.25 mg/mL U-15N; U-13C; NA-H MYDGF, 9 mM NA sodium phosphate, 135 mM NA sodium chloride, 15 uM NA DSS, 0.02 % w/v NA sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	MYDGF	[U-15N; U-13C]	8.25 mg/mL
2	sodium phosphate	natural abundance	9 mM
3	sodium chloride	natural abundance	135 mM
4	DSS	natural abundance	15 uM
5	sodium azide	natural abundance	0.02 % w/v

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: -0.12 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: -0.12 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: -0.04 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: 0.72 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6O6W, Strand ID: A Detail

Release date

2019-08-12

Citation

Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum
Bortnov, V., Tonelli, M., Lee, W., Lin, Z., Annis, D.S., Demerdash, O.N., Bateman, A., Mitchell, J.C., Ge, Y., Markley, J.L., Mosher, D.F.
Nat. Commun. (2019), 10, 5612-5612, PubMed 31819058 , DOI 10.1038/s41467-019-13577-5 , Abstract

Related entities 1. Myeloid-derived growth factor, : 2 : 5 entities Detail

Interaction partners 1. Myeloid-derived growth factor, : 7 interactors Detail

More details for 7 interactors identified by 5 citations

Experiments performed 17 experiments Detail

1 3D 1H,15N-HSQC NOESY

Instrument

Varian VNS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 8.25 mg/mL U-15N; U-13C; NA-H MYDGF, 9 mM NA sodium phosphate, 135 mM NA sodium chloride, 15 uM NA DSS, 0.02 % w/v NA sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	MYDGF	[U-15N; U-13C]	8.25 mg/mL
2	sodium phosphate	natural abundance	9 mM
3	sodium chloride	natural abundance	135 mM
4	DSS	natural abundance	15 uM
5	sodium azide	natural abundance	0.02 % w/v

2 3D 1H,13C-HSQC NOESY aliphatic

Instrument

Varian VNS - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MYDGF	[U-15N; U-13C]	8.25 mg/mL
2	sodium phosphate	natural abundance	9 mM
3	sodium chloride	natural abundance	135 mM
4	DSS	natural abundance	15 uM
5	sodium azide	natural abundance	0.02 % w/v

3 3D 1H,13C-HSQC NOESY aromatic

Instrument

Varian VNS - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MYDGF	[U-15N; U-13C]	8.25 mg/mL
2	sodium phosphate	natural abundance	9 mM
3	sodium chloride	natural abundance	135 mM
4	DSS	natural abundance	15 uM
5	sodium azide	natural abundance	0.02 % w/v

4 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MYDGF	[U-15N; U-13C]	8.25 mg/mL
2	sodium phosphate	natural abundance	9 mM
3	sodium chloride	natural abundance	135 mM
4	DSS	natural abundance	15 uM
5	sodium azide	natural abundance	0.02 % w/v

5 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MYDGF	[U-15N; U-13C]	8.25 mg/mL
2	sodium phosphate	natural abundance	9 mM
3	sodium chloride	natural abundance	135 mM
4	DSS	natural abundance	15 uM
5	sodium azide	natural abundance	0.02 % w/v

6 2D 1H-13C HSQC aromatic

Instrument

Varian VNS - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MYDGF	[U-15N; U-13C]	8.25 mg/mL
2	sodium phosphate	natural abundance	9 mM
3	sodium chloride	natural abundance	135 mM
4	DSS	natural abundance	15 uM
5	sodium azide	natural abundance	0.02 % w/v

7 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MYDGF	[U-15N; U-13C]	8.25 mg/mL
2	sodium phosphate	natural abundance	9 mM
3	sodium chloride	natural abundance	135 mM
4	DSS	natural abundance	15 uM
5	sodium azide	natural abundance	0.02 % w/v

8 3D HNCACB

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MYDGF	[U-15N; U-13C]	8.25 mg/mL
2	sodium phosphate	natural abundance	9 mM
3	sodium chloride	natural abundance	135 mM
4	DSS	natural abundance	15 uM
5	sodium azide	natural abundance	0.02 % w/v

9 3D HNCO

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MYDGF	[U-15N; U-13C]	8.25 mg/mL
2	sodium phosphate	natural abundance	9 mM
3	sodium chloride	natural abundance	135 mM
4	DSS	natural abundance	15 uM
5	sodium azide	natural abundance	0.02 % w/v

10 3D C(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MYDGF	[U-15N; U-13C]	8.25 mg/mL
2	sodium phosphate	natural abundance	9 mM
3	sodium chloride	natural abundance	135 mM
4	DSS	natural abundance	15 uM
5	sodium azide	natural abundance	0.02 % w/v

11 3D HBHA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MYDGF	[U-15N; U-13C]	8.25 mg/mL
2	sodium phosphate	natural abundance	9 mM
3	sodium chloride	natural abundance	135 mM
4	DSS	natural abundance	15 uM
5	sodium azide	natural abundance	0.02 % w/v

12 3D HCCH-TOCSY aliphatic

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MYDGF	[U-15N; U-13C]	8.25 mg/mL
2	sodium phosphate	natural abundance	9 mM
3	sodium chloride	natural abundance	135 mM
4	DSS	natural abundance	15 uM
5	sodium azide	natural abundance	0.02 % w/v

13 3D H(CCO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MYDGF	[U-15N; U-13C]	8.25 mg/mL
2	sodium phosphate	natural abundance	9 mM
3	sodium chloride	natural abundance	135 mM
4	DSS	natural abundance	15 uM
5	sodium azide	natural abundance	0.02 % w/v

14 2D (HB)CB(CGCD)HD aromatic

Instrument

Varian VNS - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MYDGF	[U-15N; U-13C]	8.25 mg/mL
2	sodium phosphate	natural abundance	9 mM
3	sodium chloride	natural abundance	135 mM
4	DSS	natural abundance	15 uM
5	sodium azide	natural abundance	0.02 % w/v

15 2D (HB)CB(CGCDCE)HDHE aromatic

Instrument

Varian VNS - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MYDGF	[U-15N; U-13C]	8.25 mg/mL
2	sodium phosphate	natural abundance	9 mM
3	sodium chloride	natural abundance	135 mM
4	DSS	natural abundance	15 uM
5	sodium azide	natural abundance	0.02 % w/v

16 3D HCCH-TOCSY aromatic

Instrument

Varian VNS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MYDGF	[U-15N; U-13C]	8.25 mg/mL
2	sodium phosphate	natural abundance	9 mM
3	sodium chloride	natural abundance	135 mM
4	DSS	natural abundance	15 uM
5	sodium azide	natural abundance	0.02 % w/v

17 3D 1H,15N-HSQC NOESY 1H,13C-HSQC

Instrument

Bruker AvanceIII - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MYDGF	[U-15N; U-13C]	8.25 mg/mL
2	sodium phosphate	natural abundance	9 mM
3	sodium chloride	natural abundance	135 mM
4	DSS	natural abundance	15 uM
5	sodium azide	natural abundance	0.02 % w/v

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30584_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)
1:37:CYS:SG	1:66:CYS:SG	oxidized, CA 53.64, CB 43.165 ppm	oxidized, CA 52.754, CB 42.999 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr30584_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1751		100.0 (chain: 1, length: 147)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 147, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 972
  - ¹³C chemical shifts: 630
  - ¹⁵N chemical shifts: 149
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	863	832	96.4
¹³C chemical shifts	662	630	95.2
¹⁵N chemical shifts	157	149	94.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	300	298	99.3
¹³C chemical shifts	294	285	96.9
¹⁵N chemical shifts	141	139	98.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	563	534	94.8
¹³C chemical shifts	368	345	93.8
¹⁵N chemical shifts	16	10	62.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	70	95.9
¹³C chemical shifts	73	70	95.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	91	71	78.0
¹³C chemical shifts	89	69	77.5
¹⁵N chemical shifts	2	2	100.0

Keywords Endoplasmic Reticulum, UNKNOWN FUNCTION, UPF0556

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Found 1 Document (0.766 seconds)

BMRB: 30584

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Myeloid-derived growth factor, : 2 : 5 entities Detail

Interaction partners 1. Myeloid-derived growth factor, : 7 interactors Detail

Experiments performed 17 experiments Detail

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Chemical shift validation 3 contents Detail