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BMRB: 25149

2MT5

Isolated Ring domain

Authors

Brown, N.G., Watson, E.R., Weissman, F., Royappa, G., Schulman, B., Jarvis, M., Vanderlinden, R., Frye, J.J., Qiao, R., Petzold, G., Peters, J., Stark, H.

Assembly

Isolated Ring domain

Entity

1. Isolated Ring domain, entity 1 (polymer, Thiol state: all free), 70 monomers, 8039.265 Da Detail

GSVANDENCG ICRMAFNGCC PDCKVPGDDC PLVWGQCSHC FHMHCILKWL HAQQVQQHCP MCRQEWKFKE

2. ZINC ION (non-polymer), 65.409 × 3 Da

Total weight

8235.492 Da

Max. entity weight

8039.265 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.5 %, Completeness (bb): 97.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.5 % (790 of 810)	99.1 % (421 of 425)	95.4 % (293 of 307)	97.4 % (76 of 78)
Backbone	97.6 % (402 of 412)	98.6 % (139 of 141)	97.1 % (199 of 205)	97.0 % (64 of 66)
Sidechain	97.6 % (452 of 463)	99.3 % (282 of 284)	94.6 % (158 of 167)	100.0 % (12 of 12)
Aromatic	93.0 % (80 of 86)	100.0 % (43 of 43)	85.0 % (34 of 40)	100.0 % (3 of 3)
Methyl	95.2 % (40 of 42)	100.0 % (21 of 21)	90.5 % (19 of 21)

1. entity 1

GSVANDENCG ICRMAFNGCC PDCKVPGDDC PLVWGQCSHC FHMHCILKWL HAQQVQQHCP MCRQEWKFKE

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.5 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

LACS Plot; CA

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

Referencing offset: -0.38 ppm, Outliers: 2 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
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.38 ppm, Outliers: 2 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
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.15 ppm, Outliers: 1 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
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.17 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MT5, Strand ID: A Detail

Release date

2014-10-26

Citation

Mechanism of polyubiquitination by human anaphase-promoting complex: RING repurposing for ubiquitin chain assembly
Brown, N.G., Watson, E.R., Weissman, F., Royappa, G., Jarvis, M., Vanderlinden, R., Frye, J.J., Qiao, R., Petzold, G., Peters, J., Stark, H., Schulman, B.
Mol. Cell (2014), 56, 246-260, PubMed 25306923 , DOI 10.1016/j.molcel.2014.09.009 , Abstract

Entries sharing articles EMDB: 2 entries Detail

  EMDB: 2775 released on 2014-10-08
    Title Mechanism of polyubiquitination by human Anaphase Promoting Complex: RING repurposing for ubiquitin chain assembly
  EMDB: 6084 released on 2014-10-01
    Title Anaphase Promoting Complex with bound Ube2S

Related entities 1. Isolated Ring domain, entity 1, : 1 : 1 : 23 : 203 entities Detail

Interaction partners 1. Isolated Ring domain, entity 1, : 15 interactors Detail

More details for 15 interactors identified by 6 citations

Experiments performed 6 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25149_2mt5.nef
Input source #2: Coordindates	2mt5.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
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

None

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)
1:30:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:45:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:37:CYS:SG	2:3:ZN:ZN	unknown	unknown	n/a
1:59:CYS:SG	2:3:ZN:ZN	unknown	unknown	n/a
1:62:CYS:SG	2:3:ZN:ZN	unknown	unknown	n/a
1:9:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:23:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:12:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None
B	2	ZN	ZINC ION	None
B	3	ZN	ZINC ION	None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70
GSVANDENCGICRMAFNGCCPDCKVPGDDCPLVWGQCSHCFHMHCILKWLHAQQVQQHCPMCRQEWKFKE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSVANDENCGICRMAFNGCCPDCKVPGDDCPLVWGQCSHCFHMHCILKWLHAQQVQQHCPMCRQEWKFKE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	70	0	0	100.0

Content subtype: combined_25149_2mt5.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	8		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	789		100.0 (chain: A, length: 70)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1412 (1)	noe	97.1 (chain: A, length: 70)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	31 (31)	.	51.4 (chain: A, 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: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 421
  - ¹³C chemical shifts: 292
  - ¹⁵N chemical shifts: 76
- 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	425	421	99.1
¹³C chemical shifts	307	292	95.1
¹⁵N chemical shifts	80	76	95.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	141	139	98.6
¹³C chemical shifts	140	134	95.7
¹⁵N chemical shifts	66	64	97.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	284	282	99.3
¹³C chemical shifts	167	158	94.6
¹⁵N chemical shifts	14	12	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	24	100.0
¹³C chemical shifts	24	22	91.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	43	43	100.0
¹³C chemical shifts	40	34	85.0
¹⁵N chemical shifts	3	3	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: 70, Sequence coverage: 97.1%
- Total number of restraints: 1412
- Weight of restraints: 1.0 (1412)
- Potential type of restraints: upper-bound-parabolic (1412)
- Range of distance target values: 2.39, 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
    None
- 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: 70, Sequence coverage: 51.4%
- Total number of restraints: 31
- Total number of restraints per polymer type: 31
- Weight of restraints: 1.0 (31)
- Potential type of restraints: square-well-parabolic (31)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Ring domain, zinc binding domain

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Found 1 Document (0.892 seconds)

BMRB: 25149

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles EMDB: 2 entries Detail

Related entities 1. Isolated Ring domain, entity 1, : 1 : 1 : 23 : 203 entities Detail

Interaction partners 1. Isolated Ring domain, entity 1, : 15 interactors Detail

Experiments performed 6 experiments Detail

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NMR combined restraints 4 contents Detail