BMRBj - BMREntryMaster

Found 1 Document (0.807 seconds)

BMRB: 30899

7MLA

Solution NMR structure of HDMX in complex with Zn and MCo-52-2

Authors

Ramirez, L.S., Theophall, G., Chaudhuri, D., Camarero, J.C., Shekhtman, A.

Assembly

Protein Mdm4, MCo-52-2

Entity

1. Protein Mdm4, MCo-52-2, entity 1 (polymer, Thiol state: free and other bound), 70 monomers, 7781.166 Da Detail

GSHMYSGEDC QNLLKPCSLC EKRPRDGNII HGRTGHLVTC FHCARRLKKA GASCPICKKE IQLVIKVFIA

2. Protein Mdm4, MCo-52-2, entity 2 (polymer, Thiol state: all disulfide bound), 34 monomers, 3594.007 Da Detail

GGVCPNLYLL CRRDSDCPGA CICRHDSYCG SGSD

3. Protein Mdm4, MCo-52-2, entity ZN (non-polymer), 65.409 × 2 Da

Total weight

11505.991 Da

Max. entity weight

7781.166 Da

Entity Connection

disulfide 11, covalent 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	2:CYS4:SG	2:CYS21:SG
2	disulfide	sing	2:CYS11:SG	2:CYS23:SG
3	disulfide	sing	2:CYS17:SG	2:CYS29:SG
4	covalent	sing	2:GLY1:SG	2:ASP34:SG
5	disulfide	sing	1:CYS17:SG	3:ZN1:ZN
6	disulfide	sing	1:CYS20:SG	3:ZN1:ZN
7	disulfide	sing	1:CYS40:SG	3:ZN1:ZN
8	disulfide	sing	1:CYS43:SG	3:ZN1:ZN
9	disulfide	sing	1:HIS31:SG	3:ZN1:ZN
10	disulfide	sing	1:HIS36:SG	3:ZN1:ZN
11	disulfide	sing	1:CYS54:SG	3:ZN1:ZN
12	disulfide	sing	1:CYS57:SG	3:ZN1:ZN

Source organism

Homo sapiens , synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 98.1 %, Completeness: 88.0 %, Completeness (bb): 83.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.0 % (1022 of 1161)	95.0 % (574 of 604)	78.2 % (348 of 445)	89.3 % (100 of 112)
Backbone	83.2 % (511 of 614)	96.7 % (207 of 214)	69.1 % (208 of 301)	97.0 % (96 of 99)
Sidechain	94.1 % (602 of 640)	94.1 % (367 of 390)	97.5 % (231 of 237)	30.8 % (4 of 13)
Aromatic	90.6 % (58 of 64)	90.6 % (29 of 32)	90.6 % (29 of 32)
Methyl	100.0 % (94 of 94)	100.0 % (47 of 47)	100.0 % (47 of 47)

1. entity 1

GSHMYSGEDC QNLLKPCSLC EKRPRDGNII HGRTGHLVTC FHCARRLKKA GASCPICKKE IQLVIKVFIA

2. entity 2

GGVCPNLYLL CRRDSDCPGA CICRHDSYCG SGSD

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM [U-100% 13C; U-100% 15N] Hdmx, 0.100 mM MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Hdmx	[U-100% 13C; U-100% 15N]		0.100 mM
2	MCo-52-2	natural abundance		0.100 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM Hdmx, 0.100 mM [U-100% 13C; U-100% 15N] MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	Hdmx	natural abundance		0.100 mM
4	MCo-52-2	[U-100% 13C; U-100% 15N]		0.100 mM

Release date

2021-05-02

Citation

Solution NMR structure of HDMX in complex with Zn and cyclotide 52-2
Chaudhuri, D., Ramirez, L.S., Theophall, G., Shekhtman, A., Camarero, J.C.

Related entities 1. Protein Mdm4, MCo-52-2, entity 1, : 2 : 62 entities Detail

Related entities 2. Protein Mdm4, MCo-52-2, entity 2, : 1 : 47 entities Detail

Interaction partners 1. Protein Mdm4, MCo-52-2, entity 1, : 32 interactors Detail

More details for 32 interactors identified by 13 citations

Experiments performed 20 experiments Detail

1 3D HNCA

Instrument

Bruker Ascend - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM [U-100% 13C; U-100% 15N] Hdmx, 0.100 mM MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Hdmx	[U-100% 13C; U-100% 15N]		0.100 mM
2	MCo-52-2	natural abundance		0.100 mM

2 2D 1H-13C HSQC

Instrument

Bruker Ascend - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM [U-100% 13C; U-100% 15N] Hdmx, 0.100 mM MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Hdmx	[U-100% 13C; U-100% 15N]		0.100 mM
2	MCo-52-2	natural abundance		0.100 mM

3 2D 1H-15N HSQC

Instrument

Bruker Ascend - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM [U-100% 13C; U-100% 15N] Hdmx, 0.100 mM MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Hdmx	[U-100% 13C; U-100% 15N]		0.100 mM
2	MCo-52-2	natural abundance		0.100 mM

4 3D 1H-13C NOESY

Instrument

Bruker Ascend - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM [U-100% 13C; U-100% 15N] Hdmx, 0.100 mM MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Hdmx	[U-100% 13C; U-100% 15N]		0.100 mM
2	MCo-52-2	natural abundance		0.100 mM

5 3D 1H-15N NOESY

Instrument

Bruker Ascend - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM [U-100% 13C; U-100% 15N] Hdmx, 0.100 mM MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Hdmx	[U-100% 13C; U-100% 15N]		0.100 mM
2	MCo-52-2	natural abundance		0.100 mM

6 3D HCCH-TOCSY

Instrument

Bruker Ascend - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM [U-100% 13C; U-100% 15N] Hdmx, 0.100 mM MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Hdmx	[U-100% 13C; U-100% 15N]		0.100 mM
2	MCo-52-2	natural abundance		0.100 mM

7 3D HBHA(CO)NH

Instrument

Bruker Ascend - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM [U-100% 13C; U-100% 15N] Hdmx, 0.100 mM MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Hdmx	[U-100% 13C; U-100% 15N]		0.100 mM
2	MCo-52-2	natural abundance		0.100 mM

8 3D HN(CO)CA

Instrument

Bruker Ascend - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM [U-100% 13C; U-100% 15N] Hdmx, 0.100 mM MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Hdmx	[U-100% 13C; U-100% 15N]		0.100 mM
2	MCo-52-2	natural abundance		0.100 mM

9 3D HNCACB

Instrument

Bruker Ascend - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM [U-100% 13C; U-100% 15N] Hdmx, 0.100 mM MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Hdmx	[U-100% 13C; U-100% 15N]		0.100 mM
2	MCo-52-2	natural abundance		0.100 mM

10 3D CBCA(CO)NH

Instrument

Bruker Ascend - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM [U-100% 13C; U-100% 15N] Hdmx, 0.100 mM MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Hdmx	[U-100% 13C; U-100% 15N]		0.100 mM
2	MCo-52-2	natural abundance		0.100 mM

11 2D 1H-13C HSQC

Instrument

Bruker Ascend - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM Hdmx, 0.100 mM [U-100% 13C; U-100% 15N] MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	Hdmx	natural abundance		0.100 mM
4	MCo-52-2	[U-100% 13C; U-100% 15N]		0.100 mM

12 2D 1H-15N HSQC

Instrument

Bruker Ascend - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM Hdmx, 0.100 mM [U-100% 13C; U-100% 15N] MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	Hdmx	natural abundance		0.100 mM
4	MCo-52-2	[U-100% 13C; U-100% 15N]		0.100 mM

13 3D 1H-13C NOESY

Instrument

Bruker Ascend - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM Hdmx, 0.100 mM [U-100% 13C; U-100% 15N] MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	Hdmx	natural abundance		0.100 mM
4	MCo-52-2	[U-100% 13C; U-100% 15N]		0.100 mM

14 3D 1H-15N NOESY

Instrument

Bruker Ascend - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM Hdmx, 0.100 mM [U-100% 13C; U-100% 15N] MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	Hdmx	natural abundance		0.100 mM
4	MCo-52-2	[U-100% 13C; U-100% 15N]		0.100 mM

15 3D HCCH-TOCSY

Instrument

Bruker Ascend - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM Hdmx, 0.100 mM [U-100% 13C; U-100% 15N] MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	Hdmx	natural abundance		0.100 mM
4	MCo-52-2	[U-100% 13C; U-100% 15N]		0.100 mM

16 3D HNCA

Instrument

Bruker Ascend - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM Hdmx, 0.100 mM [U-100% 13C; U-100% 15N] MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	Hdmx	natural abundance		0.100 mM
4	MCo-52-2	[U-100% 13C; U-100% 15N]		0.100 mM

17 3D CBCA(CO)NH

Instrument

Bruker Ascend - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM Hdmx, 0.100 mM [U-100% 13C; U-100% 15N] MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	Hdmx	natural abundance		0.100 mM
4	MCo-52-2	[U-100% 13C; U-100% 15N]		0.100 mM

18 3D HNCACB

Instrument

Bruker Ascend - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM Hdmx, 0.100 mM [U-100% 13C; U-100% 15N] MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	Hdmx	natural abundance		0.100 mM
4	MCo-52-2	[U-100% 13C; U-100% 15N]		0.100 mM

19 3D HN(CO)CA

Instrument

Bruker Ascend - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM Hdmx, 0.100 mM [U-100% 13C; U-100% 15N] MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	Hdmx	natural abundance		0.100 mM
4	MCo-52-2	[U-100% 13C; U-100% 15N]		0.100 mM

20 3D H(CCO)NH

Instrument

Bruker Ascend - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.100 mM [U-100% 13C; U-100% 15N] Hdmx, 0.100 mM MCo-52-2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Hdmx	[U-100% 13C; U-100% 15N]		0.100 mM
2	MCo-52-2	natural abundance		0.100 mM

Chemical shift validation 5 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30899_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	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Error

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
2:4:CYS:SG	2:21:CYS:SG	oxidized, CA 53.38, CB 41.834 ppm	oxidized, CA 56.739, CB 46.597 ppm	n/a
2:11:CYS:SG	2:23:CYS:SG	oxidized, CA 53.716, CB 48.045 ppm	oxidized, CA 55.263, CB 38.277 ppm	n/a
2:17:CYS:SG	2:29:CYS:SG	oxidized, CA 52.085, CB 40.754 ppm	oxidized, CA 55.781, CB 40.374 ppm	n/a
2:1:GLY:SG	2:34:ASP:SG	unknown	unknown	n/a

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)
1:17:CYS:SG	3:1:ZN:ZN	oxidized 5.5%, reduced 94.5%, CA 60.912, CB 32.624 ppm	unknown	n/a
1:20:CYS:SG	3:1:ZN:ZN	oxidized 8.2%, reduced 91.8%, CA 59.483, CB 32.263 ppm	unknown	n/a
1:40:CYS:SG	3:1:ZN:ZN	oxidized 75.3%, reduced 24.7%, CA 58.355, CB 34.134 ppm	unknown	n/a
1:43:CYS:SG	3:1:ZN:ZN	reduced, CA 65.651, CB 29.643 ppm	unknown	n/a
1:31:HIS:SG	4:1:ZN:ZN	unknown	unknown	n/a
1:36:HIS:SG	4:1:ZN:ZN	unknown	unknown	n/a
1:54:CYS:SG	4:1:ZN:ZN	reduced, CA 57.915, CB 30.949 ppm	unknown	n/a
1:57:CYS:SG	4:1:ZN:ZN	oxidized 18.4%, reduced 81.6%, CA 58.29, CB 32.421 ppm	unknown	n/a

Non-standard residues

None

Content subtype: bmr30899_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1100		100.0 (chain: 2, length: 34), 97.1 (chain: 1, length: 70)
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: 2, Chain length: 34, Sequence coverage: 100.0%
  - Entity_assembly_ID: 1, Chain length: 70, Sequence coverage: 97.1%
- Total number of assignments
  - ¹H chemical shifts: 668
  - ¹³C chemical shifts: 332
  - ¹⁵N chemical shifts: 100
- Completeness of assignments
  - Entity_assemble_ID: 2
  - 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: 2
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	176	176	100.0
¹³C chemical shifts	131	97	74.0
¹⁵N chemical shifts	36	36	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	71	71	100.0
¹³C chemical shifts	68	34	50.0
¹⁵N chemical shifts	32	32	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	105	105	100.0
¹³C chemical shifts	63	63	100.0
¹⁵N chemical shifts	4	4	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	11	11	100.0
¹³C chemical shifts	11	11	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	10	100.0
¹³C chemical shifts	10	10	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	428	398	93.0
¹³C chemical shifts	314	235	74.8
¹⁵N chemical shifts	76	64	84.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	143	136	95.1
¹³C chemical shifts	140	67	47.9
¹⁵N chemical shifts	67	64	95.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	285	262	91.9
¹³C chemical shifts	174	168	96.6
¹⁵N chemical shifts	9	0	0.0

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	22	19	86.4
¹³C chemical shifts	22	19	86.4

Keywords Cyclotide, E3 Ligase, LIGASE, Zinc-binding protein

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Found 1 Document (0.807 seconds)

BMRB: 30899

Sample #1

Sample #2

Related entities 1. Protein Mdm4, MCo-52-2, entity 1, : 2 : 62 entities Detail

Related entities 2. Protein Mdm4, MCo-52-2, entity 2, : 1 : 47 entities Detail

Interaction partners 1. Protein Mdm4, MCo-52-2, entity 1, : 32 interactors Detail

Experiments performed 20 experiments Detail

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Chemical shift validation 5 contents Detail