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BMRB: 19147

2M6N

ZINC Binding Domain

Authors

Frye, J.J., Brown, N.G., Petzold, G., Watson, E.R., Royappa, G.R., Nourse, A., Jarvis, M., Kriwacki, R.W., Peters, J., Stark, H., Schulman, B.A.

Assembly

APC/C CDH1-EMI1: multimodal mechanism of E3 ligase shutdown

Entity

1. APC/C CDH1-EMI1 (polymer, Thiol state: free and other bound), 86 monomers, 9584.184 Da Detail

GSEVAKTLKK NESLKACIRC NSPAKYDCYL QRATCKREGC GFDYCTKCLC NYHTTKDCSD GKLLKASCKI GPLPGTKKSK KNLRRL

2. ZINC ION (non-polymer, Thiol state: not present), 65.409 × 2 Da

Total weight

9715.002 Da

Max. entity weight

9584.184 Da

Entity Connection

na 7 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS17:SG	2:ZN1:ZN
2	na	sing	1:CYS20:SG	2:ZN1:ZN
3	na	sing	1:CYS35:SG	2:ZN1:ZN
4	na	sing	1:CYS40:SG	2:ZN1:ZN
5	na	sing	1:CYS45:SG	2:ZN1:ZN
6	na	sing	1:CYS48:SG	2:ZN1:ZN
7	na	sing	1:CYS58:SG	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.8 %, Completeness: 96.6 %, Completeness (bb): 97.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.6 % (967 of 1001)	98.7 % (525 of 532)	93.4 % (356 of 381)	97.7 % (86 of 88)
Backbone	97.1 % (495 of 510)	97.7 % (171 of 175)	96.4 % (243 of 252)	97.6 % (81 of 83)
Sidechain	96.7 % (552 of 571)	99.2 % (354 of 357)	92.3 % (193 of 209)	100.0 % (5 of 5)
Aromatic	78.3 % (36 of 46)	100.0 % (23 of 23)	56.5 % (13 of 23)
Methyl	91.4 % (64 of 70)	100.0 % (35 of 35)	82.9 % (29 of 35)

1. APC/C CDH1-EMI1

GSEVAKTLKK NESLKACIRC NSPAKYDCYL QRATCKREGC GFDYCTKCLC NYHTTKDCSD GKLLKASCKI GPLPGTKKSK KNLRRL

Show sample condition

Sample

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

#	Name	Isotope labeling	Concentration
1	APC/C_CDH1-EMI1	[U-100% 13C; U-100% 15N]	0.8 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
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.35 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: 0.35 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: 0.05 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.24 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M6N, Strand ID: A Detail

Release date

2015-08-31

Citation

EM Structure of APC/C_CDH1-EMI1: multimodal mechanism of E3 ligase shutdown
Frye, J., Brown, N., Petzold, G., Watson, E., Royappa, G., Nourse, A., Jarvis, M., Kriwacki, R., Peters, J., Stark, H., Schulman, B.
Nat. Struct. Biol.

Related entities 1. APC/C CDH1-EMI1, : 1 : 3 : 18 entities Detail

Interaction partners 1. APC/C CDH1-EMI1, : 25 interactors Detail

More details for 25 interactors identified by 10 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC