BMRBj - BMREntryMaster

Found 1 Document (1.474 seconds)

BMRB: 18221

2LOQ

Backbone structure of human membrane protein FAM14B (Interferon alpha-inducible protein 27-like protein 1)

Authors

Klammt, C., Chui, E.JC., Maslennikov, I., Kwiatkowski, W., Choe, S.

Assembly

FAM14B

Entity

1. FAM14B (polymer, Thiol state: not present), 113 monomers, 10557.18 Da Detail

MTSLYKKVGM GKESGWDSGR AAVAAVVGGV VAVGTVLVAL SAMGFTSVGI AASSIAAKMM STAAIANGGG VAAGSLVAIL QSVGAAGLSV TSKVIGGFAG TALGAWLGSP PSS

Formula weight

10557.18 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.3 %, Completeness: 73.8 %, Completeness (bb): 91.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	73.8 % (827 of 1120)	64.4 % (357 of 554)	80.3 % (362 of 451)	93.9 % (108 of 115)
Backbone	91.2 % (615 of 674)	84.8 % (207 of 244)	94.0 % (300 of 319)	97.3 % (108 of 111)
Sidechain	55.7 % (300 of 539)	48.4 % (150 of 310)	66.7 % (150 of 225)	0.0 % (0 of 4)
Aromatic	1.9 % (1 of 52)	3.8 % (1 of 26)	0.0 % (0 of 24)	0.0 % (0 of 2)
Methyl	67.3 % (113 of 168)	64.3 % (54 of 84)	70.2 % (59 of 84)

1. entity

MTSLYKKVGM GKESGWDSGR AAVAAVVGGV VAVGTVLVAL SAMGFTSVGI AASSIAAKMM STAAIANGGG VAAGSLVAIL QSVGAAGLSV TSKVIGGFAG TALGAWLGSP PSS

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 6.0, Details U-15N-labeled protein

#	Name	Isotope labeling	Concentration
1	MES-Bis-TRIS	natural abundance	20 mM
2	LMPG	natural abundance	3 %
3	DSS	natural abundance	0.5 mM
4	D2O	natural abundance	5 %
5	H2O	natural abundance	95 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 6.0, Details U-15N-13C-labeled protein

#	Name	Isotope labeling	Concentration
6	MES-Bis-TRIS	natural abundance	20 mM
7	LMPG	natural abundance	3 %
8	DSS	natural abundance	0.5 mM
9	D2O	natural abundance	5 %
10	H2O	natural abundance	95 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 6.0, Details U-15N-13C-2H-labeled protein

#	Name	Isotope labeling	Concentration
11	MES-Bis-TRIS	natural abundance	20 mM
12	LMPG	natural abundance	3 %
13	DSS	natural abundance	0.5 mM
14	D2O	natural abundance	5 %
15	H2O	natural abundance	95 %

Sample #4

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 6.0, Details U-15N-2H-labeled protein

#	Name	Isotope labeling	Concentration
16	MES-Bis-TRIS	natural abundance	20 mM
17	LMPG	natural abundance	3 %
18	DSS	natural abundance	0.5 mM
19	D2O	natural abundance	5 %
20	H2O	natural abundance	95 %

Sample #5

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 6.0, Details Combinatorial residue-selective 15N-13C1-labeled protein

#	Name	Isotope labeling	Concentration
21	MES-Bis-TRIS	natural abundance	20 mM
22	LMPG	natural abundance	3 %
23	DSS	natural abundance	0.5 mM
24	D2O	natural abundance	5 %
25	H2O	natural abundance	95 %

Sample #6

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 6.0, Details Single-cysteine U-15N-labeled mutants with paramagnetic spin label MTSL

#	Name	Isotope labeling	Concentration
26	MES-Bis-TRIS	natural abundance	20 mM
27	LMPG	natural abundance	3 %
28	DSS	natural abundance	0.5 mM
29	D2O	natural abundance	5 %
30	H2O	natural abundance	95 %

Sample #7

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 6.0, Details Single-cysteine U-15N-labeled mutants with diamagnetic analog of MTSL

#	Name	Isotope labeling	Concentration
31	MES-Bis-TRIS	natural abundance	20 mM
32	LMPG	natural abundance	3 %
33	DSS	natural abundance	0.5 mM
34	D2O	natural abundance	5 %
35	H2O	natural abundance	95 %

Protein Blocks Logo

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

Release date

2012-05-21

Citation

Facile backbone structure determination of human membrane proteins by NMR spectroscopy
Klammt, C., Maslennikov, I., Bayrhuber, M., Eichmann, C., Vajpai, N., Chiu, E., Blain, K.Y., Esquivies, L., Kwon, J., Balana, B., Pieper, U., Sali, A., Slesinger, P.A., Kwiatkowski, W., Riek, R., Choe, S.
Nat. Methods (2012), 9, 834-839, PubMed 22609626 , DOI 10.1038/nmeth.2033 , Abstract

Entries sharing articles BMRB: 6, Swiss-Prot: 6 entries Detail

  BMRB: 18217 released on 2012-05-21
    Title Backbone structure of human membrane protein HIGD1A
  BMRB: 18218 released on 2012-05-21
    Title Backbone structure of human membrane protein HIGD1B
  BMRB: 18219 released on 2012-05-21
    Title Backbone structure of human membrane protein TMEM14A from NOE data
  BMRB: 18220 released on 2012-05-21
    Title Backbone structure of human membrane protein TMEM14A
  BMRB: 18222 released on 2012-05-21
    Title Backbone structure of human membrane protein TMEM141
  BMRB: 18223 released on 2012-05-21
    Title Backbone structure of human membrane protein TMEM14C
  Swiss-Prot: Q96I45 released on 2007-03-06
    Title TM141_HUMAN Entity Transmembrane protein 141
  Swiss-Prot: Q9P298 released on 2005-09-27
    Title HIG1B_HUMAN Entity HIG1 domain family member 1B
  Swiss-Prot: Q9Y241 released on 2005-09-27
    Title HIG1A_HUMAN Entity HIG1 domain family member 1A, mitochondrial
  Swiss-Prot: Q96BM0 released on 2003-01-17
    Title I27L1_HUMAN Entity Interferon alpha-inducible protein 27-like protein 1
  Swiss-Prot: Q9P0S9 released on 2003-01-10
    Title TM14C_HUMAN Entity Transmembrane protein 14C
  Swiss-Prot: Q9Y6G1 released on 2000-12-01
    Title TM14A_HUMAN Entity Transmembrane protein 14A

Related entities 1. FAM14B, : 1 : 2 : 7 entities Detail

Experiments performed 10 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18221_2loq.nef
Input source #2: Coordindates	2loq.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	Warning

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--------90-
MTSLYKKVGMGKESGWDSGRAAVAAVVGGVVAVGTVLVALSAMGFTSVGIAASSIAAKMMSTAAIANGGGVAAGSLVAILQSVGAAGLSVTSKVIGGFAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MTSLYKKVGMGKESGWDSGRAAVAAVVGGVVAVGTVLVALSAMGFTSVGIAASSIAAKMMSTAAIANGGGVAAGSLVAILQSVGAAGLSVTSKVIGGFAG
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

------100----
TALGAWLGSPPSS
|||||||||||||
TALGAWLGSPPSS
-------110---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	113	0	0	100.0

Content subtype: combined_18221_2loq.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	787		95.6 (chain: A, length: 113)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	269 (1)	undefined	85.8 (chain: A, length: 113)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	423 (1)	undefined	88.5 (chain: A, length: 113)
3	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	200 (1)	hbond	48.7 (chain: A, length: 113)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 95.6%
- Total number of assignments
  - ¹H chemical shifts: 330
  - ¹³C chemical shifts: 350
  - ¹⁵N chemical shifts: 107
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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)
58	ASN	CG	176.897

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	554	330	59.6
¹³C chemical shifts	451	349	77.4
¹⁵N chemical shifts	116	107	92.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	244	199	81.6
¹³C chemical shifts	226	207	91.6
¹⁵N chemical shifts	111	107	96.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	310	131	42.3
¹³C chemical shifts	225	142	63.1
¹⁵N chemical shifts	5	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	89	49	55.1
¹³C chemical shifts	89	58	65.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	1	3.8
¹³C chemical shifts	24	0	0.0
¹⁵N chemical shifts	2	0	0.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 85.8%
- Total number of restraints: 269
- Weight of restraints: 1.0 (269)
- Potential type of restraints: upper-bound-parabolic (269)
- Range of distance target values: 12.0, 29.4 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: OK
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 88.5%
  - Total number of restraints: 423
  - Weight of restraints: 1.0 (423)
  - Potential type of restraints: lower-bound-parabolic (423)
  - Range of distance target values: 6.1, 25.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_4
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 48.7%
    - Total number of restraints: 200
    - Weight of restraints: 1.0 (200)
    - Potential type of restraints: upper-bound-parabolic (200)
    - Range of distance target values: 1.8, 3.0 (Å)
    - Histogram of distance target values
    - Histogram of discrepancy in distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Keywords Backbone structure, Helical bundle, Homo sapiens, Membrane protein, Paramagnetic relaxation enhancement

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (1.474 seconds)

BMRB: 18221

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Sample #6

Sample #7

Entries sharing articles BMRB: 6, Swiss-Prot: 6 entries Detail

Related entities 1. FAM14B, : 1 : 2 : 7 entities Detail

Experiments performed 10 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail