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Found 1 Document (2.258 seconds)

BMRB: 34030

5LNF

Solution NMR structure of farnesylated PEX19, C-terminal domain

Authors

Emmanouilidis, L., Schuetz, U., Tripsianes, K., Madl, T., Radke, J., Rucktaeschel, R., Wilmanns, M., Schliebs, W., Erdmann, R., Sattler, M.

Assembly

Peroxisomal biogenesis factor 19

Entity

1. Peroxisomal biogenesis factor 19, entity 1 (polymer, Thiol state: free and other bound), 139 monomers, 15652.54 Da Detail

GMDEGDGEGN ILPIMQSIMQ NLLSKDVLYP SLKEITEKYP EWLQSHRESL PPEQFEKYQE QHSVMCKICE QFEAETPTDS ETTQKARFEM VLDLMQQLQD LGHPPKELAG EMPPGLNFDL DALNLSGPPG ASGEQCLIM

2. Peroxisomal biogenesis factor 19, entity FAR (non-polymer), 206.367 Da

Total weight

15858.907 Da

Max. entity weight

15652.54 Da

Entity Connection

covalent 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	covalent	sing	1:CYS136:SG	2:FAR1:C1

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 91.5 %, Completeness (bb): 84.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.5 % (1488 of 1627)	98.5 % (846 of 859)	79.8 % (498 of 624)	100.0 % (144 of 144)
Backbone	84.4 % (684 of 810)	98.9 % (273 of 276)	69.8 % (284 of 407)	100.0 % (127 of 127)
Sidechain	98.4 % (931 of 946)	98.3 % (573 of 583)	98.6 % (341 of 346)	100.0 % (17 of 17)
Aromatic	100.0 % (88 of 88)	100.0 % (44 of 44)	100.0 % (43 of 43)	100.0 % (1 of 1)
Methyl	100.0 % (124 of 124)	100.0 % (62 of 62)	100.0 % (62 of 62)

1. entity 1

GMDEGDGEGN ILPIMQSIMQ NLLSKDVLYP SLKEITEKYP EWLQSHRESL PPEQFEKYQE QHSVMCKICE QFEAETPTDS ETTQKARFEM VLDLMQQLQD LGHPPKELAG EMPPGLNFDL DALNLSGPPG ASGEQCLIM

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM {U-1H,13C,15N; farnesyl-[1H,12C]} PEX19, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PEX19	[U-1H; U-13C; U-15N]		1 mM
2	farnesyl	[U-1H; U-12C]		1 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM {U-2H,12C,15N; Leu-[1H,13C,15N]; farnesyl-[1H,12C]} PEX19, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	PEX19	[U-2H; U-12C; U-15N]; Leu-[1H,13C,15N]		1 mM
4	farnesyl	[U-1H; U-12C]		1 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM {U-2H,12C,15N; Lle-[1H,13C,15N]; farnesyl-[1H,12C]} PEX19, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
5	PEX19	[U-2H; U-12C; U-15N]; Lle-[1H,13C,15N]		1 mM
6	farnesyl	[U-1H; U-12C]		1 mM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM {U-2H,12C,15N; Met-[1H,13CH3,15N]; farnesyl-[1H,12C]} PEX19, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
7	PEX19	[U-2H; U-12C; U-15N]; Met-[1H,13CH3,15N]		1 mM
8	farnesyl	[U-1H; U-12C]		1 mM

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM {U-2H,12C,15N; Ile(delta1),Leu(delta),Val(gamma)-[13CH3]; farnesyl-[1H,12C]} PEX19, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
9	PEX19	[U-2H; U-12C; U-15N]; Ile(delta1),Leu(delta),Val(gamma)-[13CH3]		1 mM
10	farnesyl	[U-1H; U-12C]		1 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 5LNF, Strand ID: A Detail

Release date

2017-03-06

Citation

Allosteric modulation of peroxisomal membrane protein recognition by farnesylation of the peroxisomal import receptor PEX19
Emmanouilidis, L., Schutz, U., Tripsianes, K., Madl, T., Radke, J., Rucktaschel, R., Wilmanns, M., Schliebs, W., Erdmann, R., Sattler, M.
Nat. Commun. (2017), 8, 14635-14635, PubMed 28281558 , DOI 10.1038/ncomms14635 , Abstract

Related entities 1. Peroxisomal biogenesis factor 19, entity 1, : 1 : 3 : 1 : 21 entities Detail

Interaction partners 1. Peroxisomal biogenesis factor 19, entity 1, : 39 interactors Detail

More details for 39 interactors identified by 11 citations

Experiments performed 6 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_34030_5lnf.nef
Input source #2: Coordindates	5lnf.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)
1:136:CYS:SG	2:1:FAR:C1	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	FAR	FARNESYL	Assigned chemical shifts

Sequence alignments

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

-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260
GMDEGDGEGNILPIMQSIMQNLLSKDVLYPSLKEITEKYPEWLQSHRESLPPEQFEKYQEQHSVMCKICEQFEAETPTDSETTQKARFEMVLDLMQQLQD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GMDEGDGEGNILPIMQSIMQNLLSKDVLYPSLKEITEKYPEWLQSHRESLPPEQFEKYQEQHSVMCKICEQFEAETPTDSETTQKARFEMVLDLMQQLQD
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------270-------280-------290---------
LGHPPKELAGEMPPGLNFDLDALNLSGPPGASGEQCLIM
|||||||||||||||||||||||||||||||||||||||
LGHPPKELAGEMPPGLNFDLDALNLSGPPGASGEQCLIM
-------110-------120-------130---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	139	0	0	100.0

Content subtype: combined_34030_5lnf.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1505		100.0 (chain: A, length: 139), 100.0 (chain: B, length: 1)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	4454 (1)	noe	100.0 (chain: A, length: 139)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	187 (187)	.	77.0 (chain: A, length: 139)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	136 (136)	.	67.6 (chain: A, length: 139)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 139, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 874
  - ¹⁵N chemical shifts: 145
  - ¹³C chemical shifts: 486
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
196	THR	HG1	4.866
229	CYS	HG	2.551

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	859	853	99.3
¹⁵N chemical shifts	146	145	99.3
¹³C chemical shifts	624	474	76.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	276	275	99.6
¹⁵N chemical shifts	127	126	99.2
¹³C chemical shifts	278	134	48.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	583	578	99.1
¹⁵N chemical shifts	19	19	100.0
¹³C chemical shifts	346	340	98.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	69	98.6
¹³C chemical shifts	70	69	98.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	44	100.0
¹⁵N chemical shifts	1	1	100.0
¹³C chemical shifts	43	43	100.0

Comp_index_ID	Comp_ID
1	FAR

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 139, Sequence coverage: 100.0%
- Total number of restraints: 4431
- Weight of restraints: 1.0 (4431)
- Potential type of restraints: square-well-parabolic (4431)
- Range of distance target values: 2.06, 3.9 (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: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 139, Sequence coverage: 77.0%
- Total number of restraints: 187
- Total number of restraints per polymer type: 187
- Weight of restraints: 1.0 (187)
- Potential type of restraints: square-well-parabolic (187)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 139, Sequence coverage: 67.6%

-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260
GMDEGDGEGNILPIMQSIMQNLLSKDVLYPSLKEITEKYPEWLQSHRESLPPEQFEKYQEQHSVMCKICEQFEAETPTDSETTQKARFEMVLDLMQQLQD
                  ||  |||||     |||  || |||||||||| |||||||||||||||||||||||||||||||||||| ||||||||||||
..................MQ..LSKDV.....KEI..KY.EWLQSHRESL.PEQFEKYQEQHSVMCKICEQFEAETPTDSETTQKAR.EMVLDLMQQLQD

-------270-------280-------290---------
LGHPPKELAGEMPPGLNFDLDALNLSGPPGASGEQCLIM
||| |||||||   |||| ||||     |||     |||
LGH.PKELAGE...GLNF.LDAL.....PGA.....LIM

Total number of restraints: 136
Potential type of restraints: undefined (136)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords PEX19, allostery, chaperone, farnesylation, post translational modification

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Found 1 Document (2.258 seconds)

BMRB: 34030

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Related entities 1. Peroxisomal biogenesis factor 19, entity 1, : 1 : 3 : 1 : 21 entities Detail

Interaction partners 1. Peroxisomal biogenesis factor 19, entity 1, : 39 interactors Detail

Experiments performed 6 experiments Detail

Instrument

Sample

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Instrument

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NMR combined restraints 5 contents Detail