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Found 1 Document (1.348 seconds)

BMRB: 19961

2MP2

Solution structure of SUMO Dimer in Complex with SIM2-3 from RNF4

Authors

Xu, Y., Plechanovov, A., Simpson, P., Marchant, J., Leidecker, O., Sebastian, K., Hay, R.T., Matthews, S.J.

Assembly

SUMO Dimer in Complex with SIM2-3 from RNF4

Entity

1. SUMO Dimer in Complex with SIM2-3 from RNF4, entity 1 (polymer), 82 monomers, 9338.337 Da Detail

GTENDHINLK VAGQDGSVVQ FKIKRHTPLS KLMKAYCERQ GLSMRQIRFR FDGQPINETD TPAQLEMEDE DTIDVFQQQT GG

2. SUMO Dimer in Complex with SIM2-3 from RNF4, entity 2 (polymer), 90 monomers, 10336.46 Da Detail

GSEEKPKEGV KTENDHINLK VAGQDGSVVQ FKIKRHTPLS KLMKAYCERQ GLSMRQIRFR FDGQPINETD TPAQLEMEDE DTIDVFQQQT

3. SUMO Dimer in Complex with SIM2-3 from RNF4, entity 3 (polymer), 25 monomers, 2712.931 Da Detail

TVGDEIVDLT CESLEPVVVD LTHND

Total weight

22387.729 Da

Max. entity weight

10336.46 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 79.7 %, Completeness: 61.7 %, Completeness (bb): 51.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	61.7 % (1414 of 2291)	65.0 % (782 of 1204)	58.5 % (511 of 873)	56.5 % (121 of 214)
Backbone	51.9 % (605 of 1166)	53.8 % (215 of 400)	50.6 % (292 of 577)	51.9 % (98 of 189)
Sidechain	69.2 % (905 of 1308)	70.5 % (567 of 804)	65.8 % (315 of 479)	92.0 % (23 of 25)
Aromatic	61.2 % (71 of 116)	58.6 % (34 of 58)	63.8 % (37 of 58)
Methyl	72.2 % (140 of 194)	72.2 % (70 of 97)	72.2 % (70 of 97)

1. entity 1

GTENDHINLK VAGQDGSVVQ FKIKRHTPLS KLMKAYCERQ GLSMRQIRFR FDGQPINETD TPAQLEMEDE DTIDVFQQQT GG

2. entity 2

GSEEKPKEGV KTENDHINLK VAGQDGSVVQ FKIKRHTPLS KLMKAYCERQ GLSMRQIRFR FDGQPINETD TPAQLEMEDE DTIDVFQQQT

3. entity 3

TVGDEIVDLT CESLEPVVVD LTHND

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	0.3 mM
2	entity_2	natural abundance	0.3 mM
3	entity_3	natural abundance	1.0 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
4	entity_1	natural abundance	0.3 mM
5	entity_2	[U-99% 13C; U-99% 15N]	0.3 mM
6	entity_3	natural abundance	1.0 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	entity_1	[U-99% 13C; U-99% 15N]		0.3 mM
8	entity_2	natural abundance		0.3 mM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details the two SUMO chains are linked through an isopeptide bond

#	Name	Isotope labeling	Type	Concentration
9	entity_1	natural abundance		0.3 mM
10	entity_2	[U-99% 13C; U-99% 15N]		0.3 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 2MP2, Strand ID: A, B, C Detail

Release date

2014-06-29

Citation

Structural insight into SUMO chain recognition and manipulation by the ubiquitin ligase RNF4
Xu, Y., Plechanovov, A., Simpson, P., Marchant, J., Leidecker, O., Sebastian, K., Hay, R.T., Matthews, S.J.
Nat. Commun. (2014), 5, 4217-4217, PubMed 24969970 , DOI 10.1038/ncomms5217 , Abstract

Related entities 1. SUMO Dimer in Complex with SIM2-3 from RNF4, entity 1, : 7 : 53 entities Detail

Related entities 2. SUMO Dimer in Complex with SIM2-3 from RNF4, entity 2, : 3 : 52 entities Detail

Related entities 3. SUMO Dimer in Complex with SIM2-3 from RNF4, entity 3, : 1 : 4 : 2 : 2 entities Detail

Interaction partners 3. SUMO Dimer in Complex with SIM2-3 from RNF4, entity 3, : 10 interactors Detail

More details for 10 interactors identified by 4 citations

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	0.3 mM
2	entity_2	natural abundance	0.3 mM
3	entity_3	natural abundance	1.0 mM

2 2D 1H-15N HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
4	entity_1	natural abundance	0.3 mM
5	entity_2	[U-99% 13C; U-99% 15N]	0.3 mM
6	entity_3	natural abundance	1.0 mM

3 2D 1H-15N HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	entity_1	[U-99% 13C; U-99% 15N]		0.3 mM
8	entity_2	natural abundance		0.3 mM

4 2D 1H-15N HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details the two SUMO chains are linked through an isopeptide bond

#	Name	Isotope labeling	Type	Concentration
9	entity_1	natural abundance		0.3 mM
10	entity_2	[U-99% 13C; U-99% 15N]		0.3 mM

5 3D HNCACB

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	entity_1	[U-99% 13C; U-99% 15N]		0.3 mM
8	entity_2	natural abundance		0.3 mM

6 3D CBCA(CO)NH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	entity_1	[U-99% 13C; U-99% 15N]		0.3 mM
8	entity_2	natural abundance		0.3 mM

7 3D HCCH-TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	entity_1	[U-99% 13C; U-99% 15N]		0.3 mM
8	entity_2	natural abundance		0.3 mM

8 3D 1H-15N NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	entity_1	[U-99% 13C; U-99% 15N]		0.3 mM
8	entity_2	natural abundance		0.3 mM

NMR combined restraints 9 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_19961_2mp2.nef
Input source #2: Coordindates	2mp2.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	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Error

Disulfide bonds

None

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

--------10--------20--------30--------40--------50--------60--------70--------80--
GTENDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GTENDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90
GSEEKPKEGVKTENDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSEEKPKEGVKTENDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQT

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

-------10--------20------
TVGDEIVDLTCESLEPVVVDLTHND
|||||||||||||||||||||||||
TVGDEIVDLTCESLEPVVVDLTHND
--------10--------20-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	82	100.0
B	B	90	100.0
C	C	25	100.0

Content subtype: combined_19961_2mp2.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1362		78.0 (chain: A, length: 82), 100.0 (chain: B, length: 90)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2366 (1)	noe	97.6 (chain: A, length: 82), 96.7 (chain: B, length: 90)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	4 (1)	undefined	No information
4	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	32 (1)	pre	12.2 (chain: A, length: 82), 6.7 (chain: B, length: 90), 8.0 (chain: C, length: 25)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_7	OK	154 (154)	.	61.0 (chain: A, length: 82), 56.7 (chain: B, length: 90)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_8	OK	141 (141)	.	82.9 (chain: A, length: 82), 81.1 (chain: B, length: 90)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 82, Sequence coverage: 78.0%
  - Entity_assembly_ID: B, Chain length: 90, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 765
  - ¹⁵N chemical shifts: 113
  - ¹³C chemical shifts: 484
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
26	HIS	HD1	7.053

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	507	216	42.6
¹⁵N chemical shifts	96	17	17.7
¹³C chemical shifts	363	92	25.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	168	21	12.5
¹⁵N chemical shifts	79	4	5.1
¹³C chemical shifts	164	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	339	195	57.5
¹⁵N chemical shifts	17	13	76.5
¹³C chemical shifts	199	92	46.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	40	35	87.5
¹³C chemical shifts	40	34	85.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	14	50.0
¹³C chemical shifts	28	17	60.7

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
16	HIS	HD1	6.61
36	HIS	HD1	7.045

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	568	546	96.1
¹⁵N chemical shifts	103	96	93.2
¹³C chemical shifts	404	392	97.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	182	178	97.8
¹⁵N chemical shifts	86	84	97.7
¹³C chemical shifts	180	179	99.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	386	368	95.3
¹⁵N chemical shifts	17	12	70.6
¹³C chemical shifts	224	213	95.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	42	100.0
¹³C chemical shifts	42	42	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	17	60.7
¹³C chemical shifts	28	17	60.7

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 82, Sequence coverage: 97.6%
  - Entity_assembly_ID: B, Chain length: 90, Sequence coverage: 96.7%
- Total number of restraints: 2358
- Weight of restraints: 1.0 (2358)
- Potential type of restraints: square-well-parabolic (2358)
- Range of distance target values: 1.47, 3.88 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: undefined
  - Total number of restraints: 4
  - Weight of restraints: 1.0 (4)
  - Potential type of restraints: square-well-parabolic (4)
  - Range of distance target values: 1.35, 2.45 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
      None
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_5
    - Status: OK
    - Experiment type: pre
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 82, Sequence coverage: 12.2%
      - Entity_assembly_ID: B, Chain length: 90, Sequence coverage: 6.7%
      - Entity_assembly_ID: C, Chain length: 25, Sequence coverage: 8.0%
    - Total number of restraints: 32
    - Weight of restraints: 1.0 (32)
    - Potential type of restraints: square-well-parabolic (32)
    - Range of distance target values: 7.5, 10.0 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
      - Chain_ID: C
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_7
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 82, Sequence coverage: 61.0%
  - Entity_assembly_ID: B, Chain length: 90, Sequence coverage: 56.7%
- Total number of restraints: 154
- Total number of restraints per polymer type: 154
- Weight of restraints: 1.0 (154)
- Potential type of restraints: square-well-parabolic (154)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_8

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 82, Sequence coverage: 82.9%

--------10--------20--------30--------40--------50--------60--------70--------80--
GTENDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG
  | ||||||||| ||||||| ||| | ||||||||||||||| |||||||||| || ||| ||||||||||||||||   |
..E.DHINLKVAG.DGSVVQF.IKR.T.LSKLMKAYCERQGLS.RQIRFRFDGQ.IN.TDT.AQLEMEDEDTIDVFQQ...G

Entity_assembly_ID: B, Chain length: 90, Sequence coverage: 81.1%

--------10--------20--------30--------40--------50--------60--------70--------80--------90
GSEEKPKEGVKTENDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQT
  ||| |||||||| | |||||| |||||   | | | |||||||||| |||| |||||||||| |||||| |||||||||||||||| |
..EEK.KEGVKTEN.H.NLKVAG.DGSVV...I.R.T.LSKLMKAYCE.QGLS.RQIRFRFDGQ.INETDT.AQLEMEDEDTIDVFQQ.T

Total number of restraints: 141
Potential type of restraints: undefined (141)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None
- Chain_ID: B
  None

Keywords SUMO, Dimer, SIM, RNF4, Complex

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Found 1 Document (1.348 seconds)

BMRB: 19961

Sample #1

Sample #2

Sample #3

Sample #4

Related entities 1. SUMO Dimer in Complex with SIM2-3 from RNF4, entity 1, : 7 : 53 entities Detail

Related entities 2. SUMO Dimer in Complex with SIM2-3 from RNF4, entity 2, : 3 : 52 entities Detail

Related entities 3. SUMO Dimer in Complex with SIM2-3 from RNF4, entity 3, : 1 : 4 : 2 : 2 entities Detail

Interaction partners 3. SUMO Dimer in Complex with SIM2-3 from RNF4, entity 3, : 10 interactors Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 9 contents Detail