BMRBj - BMREntryMaster

Found 1 Document (1.285 seconds)

BMRB: 25710

2N5E

Structure of high-density lipoprotein particles

Authors

Bibow, S., Polyhach, Y., Eichmann, C., Chi, C.N., Kowal, J., Stahlberg, H., Jeschke, G., Guentert, P., Riek, R.

Assembly

high-density lipoprotein particles

Entity

1. high-density lipoprotein particles (polymer, Thiol state: not present), 167 monomers, 19430.70 × 2 Da Detail

STFSKLREQL GPVTQEFWDN LEKETEGLRQ EMSKDLEEVK AKVQPYLDDF QKKWQEEMEL YRQKVEPLGE EMRDRARAHV DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ GLLPVLESFK VSFLSALEEY TKKLNTQ

Total weight

38861.4 Da

Max. entity weight

19430.7 Da

Source organism

Escherichia coli

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.6 %, Completeness: 40.1 %, Completeness (bb): 73.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	40.1 % (808 of 2017)	21.4 % (228 of 1065)	55.3 % (429 of 776)	85.8 % (151 of 176)
Backbone	73.7 % (730 of 990)	51.8 % (173 of 334)	82.0 % (406 of 495)	93.8 % (151 of 161)
Sidechain	14.6 % (174 of 1188)	7.7 % (56 of 731)	26.7 % (118 of 442)	0.0 % (0 of 15)
Aromatic	0.0 % (0 of 130)	0.0 % (0 of 65)	0.0 % (0 of 63)	0.0 % (0 of 2)
Methyl	19.0 % (33 of 174)	16.1 % (14 of 87)	21.8 % (19 of 87)

1. entity

STFSKLREQL GPVTQEFWDN LEKETEGLRQ EMSKDLEEVK AKVQPYLDDF QKKWQEEMEL YRQKVEPLGE EMRDRARAHV DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ GLLPVLESFK VSFLSALEEY TKKLNTQ

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 316 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	0.75 mM
2	entity	stereospecific Methyl-labeling	1 mM
3	entity	selective unlabeling	1 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 2N5E, Strand ID: A, B Detail

Release date

2015-08-05

Citation

Solution structure of discoidal high-density lipoprotein particles with a shortened apolipoprotein A-I
Bibow, S., Polyhach, Y., Eichmann, C., Chi, C.N., Kowal, J., Albiez, S., McLeod, R.A., Stahlberg, H., Jeschke, G., Guntert, P., Riek, R.
Nat. Struct. Mol. Biol. (2017), 24, 187-193, PubMed 28024148 , DOI 10.1038/nsmb.3345 , Abstract

Related entities 1. high-density lipoprotein particles, : 1 : 176 entities Detail

Interaction partners 1. high-density lipoprotein particles, : 37 interactors Detail

More details for 37 interactors identified by 22 citations

Experiments performed 6 experiments Detail

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_25710_2n5e.nef
Input source #2: Coordindates	2n5e.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

----60--------70--------80--------90-------100-------110-------120-----150-------160-------170------
STFSKLREQLGPVTQEFWDNLEKETEGLRQEMSKDLEEVKAKVQPYLDDFQKKWQEEMELYRQKVEPLGEEMRDRARAHVDALRTHLAPYSDELRQRLAA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
STFSKLREQLGPVTQEFWDNLEKETEGLRQEMSKDLEEVKAKVQPYLDDFQKKWQEEMELYRQKVEPLGEEMRDRARAHVDALRTHLAPYSDELRQRLAA
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-180-------190-------200-------210-------220-------230-------240---
RLEALKENGGARLAEYHAKATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALEEYTKKLNTQ
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
RLEALKENGGARLAEYHAKATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALEEYTKKLNTQ
-------110-------120-------130-------140-------150-------160-------

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

----60--------70--------80--------90-------100-------110-------120-----150-------160-------170------
STFSKLREQLGPVTQEFWDNLEKETEGLRQEMSKDLEEVKAKVQPYLDDFQKKWQEEMELYRQKVEPLGEEMRDRARAHVDALRTHLAPYSDELRQRLAA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
STFSKLREQLGPVTQEFWDNLEKETEGLRQEMSKDLEEVKAKVQPYLDDFQKKWQEEMELYRQKVEPLGEEMRDRARAHVDALRTHLAPYSDELRQRLAA
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-180-------190-------200-------210-------220-------230-------240---
RLEALKENGGARLAEYHAKATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALEEYTKKLNTQ
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
RLEALKENGGARLAEYHAKATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALEEYTKKLNTQ
-------110-------120-------130-------140-------150-------160-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	167	0	0	100.0
B	B	167	0	0	100.0

Content subtype: combined_25710_2n5e.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	689		97.0 (chain: A, length: 167)
1	Distance restraints	DYANA/DIANA_distance_constraints_4	Error	783 (1)	pre	44.9 (chain: A, length: 167), 59.9 (chain: B, length: 167)
2	Distance restraints	DYANA/DIANA_distance_constraints_6	OK	538 (1)	noe	70.7 (chain: A, length: 167), 70.1 (chain: B, length: 167)
3	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	824 (1)	hbond	76.6 (chain: A, length: 167), 77.2 (chain: B, length: 167)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_7	OK	490 (490)	.	84.4 (chain: A, length: 167), 84.4 (chain: B, length: 167)
1	RDC restraints	DYANA/DIANA_dipolar_coupling_8	OK	226 (226)	.	66.5 (chain: A, length: 167), 66.5 (chain: B, length: 167)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 167, Sequence coverage: 97.0%
- Total number of assignments
  - ¹³C chemical shifts: 391
  - ¹H chemical shifts: 149
  - ¹⁵N chemical shifts: 149
- Completeness of assignments
  - Entity_assemble_ID: A
- 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 (%)
¹³C chemical shifts	776	391	50.4
¹H chemical shifts	1065	149	14.0
¹⁵N chemical shifts	188	149	79.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	334	308	92.2
¹H chemical shifts	334	149	44.6
¹⁵N chemical shifts	161	149	92.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	442	83	18.8
¹H chemical shifts	731	0	0.0
¹⁵N chemical shifts	27	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	90	7	7.8
¹H chemical shifts	90	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	63	0	0.0
¹H chemical shifts	65	0	0.0
¹⁵N chemical shifts	2	0	0.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_4
- Status: Error
- Experiment type: pre
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 167, Sequence coverage: 44.9%
  - Entity_assembly_ID: B, Chain length: 167, Sequence coverage: 59.9%
- Total number of restraints: 783
- Weight of restraints: 1.0 (783)
- Potential type of restraints: upper-bound-parabolic (783)
- Range of distance target values: 11.8, 28.4 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_6
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 167, Sequence coverage: 70.7%
    - Entity_assembly_ID: B, Chain length: 167, Sequence coverage: 70.1%
  - Total number of restraints: 538
  - Weight of restraints: 1.0 (538)
  - Potential type of restraints: upper-bound-parabolic (538)
  - Range of distance target values: 3.5, 8.65 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_3
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 167, Sequence coverage: 76.6%
      - Entity_assembly_ID: B, Chain length: 167, Sequence coverage: 77.2%
    - Total number of restraints: 824
    - Weight of restraints: 1.0 (824)
    - Potential type of restraints: upper-bound-parabolic (824)
    - Range of distance target values: 1.7, 3.2 (Å)
    - Histogram of distance target values
    - Histogram of discrepancy in distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_7
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 167, Sequence coverage: 84.4%
  - Entity_assembly_ID: B, Chain length: 167, Sequence coverage: 84.4%
- Total number of restraints: 490
- Total number of restraints per polymer type: 490
- Weight of restraints: 1.0 (490)
- Potential type of restraints: square-well-parabolic (490)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

RDC restraints

Saveframe: DYANA/DIANA_dipolar_coupling_8

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 167, Sequence coverage: 66.5%

----60--------70--------80--------90-------100-------110-------120-------130-------140-------150----
....KLREQLGPVTQEFW.NLEKE.EGLRQEMSK..EE.KA...PY........QEEMELYR..VE..................................
    |||||||||||||| ||||| |||||||||  || ||   ||        ||||||||  ||                                  
....KLREQLGPVTQEFW.NLEKE.EGLRQEMSK..EE.KA...PY........QEEMELYR..VE..................................

---160-------170-------180-------190-------200-------210-------220-------230-------240---
..........PYSDELRQ.LAARLEALKENGG..LAEYH..ATEHL.TL..KAKPALEDLRQGLLPVL.SFKVSFLSA...YTKKLNTQ
          |||||||| |||||||||||||  |||||  ||||| ||  ||||||||||||||||| |||||||||   ||||||||
..........PYSDELRQ.LAARLEALKENGG..LAEYH..ATEHL.TL..KAKPALEDLRQGLLPVL.SFKVSFLSA...YTKKLNTQ

Entity_assembly_ID: B, Chain length: 167, Sequence coverage: 66.5%

----60--------70--------80--------90-------100-------110-------120-------130-------140-------150----
....KLREQLGPVTQEFW.NLEKE.EGLRQEMSK..EE.KA...PY........QEEMELYR..VE..................................
    |||||||||||||| ||||| |||||||||  || ||   ||        ||||||||  ||                                  
....KLREQLGPVTQEFW.NLEKE.EGLRQEMSK..EE.KA...PY........QEEMELYR..VE..................................

---160-------170-------180-------190-------200-------210-------220-------230-------240---
..........PYSDELRQ.LAARLEALKENGG..LAEYH..ATEHL.TL..KAKPALEDLRQGLLPVL.SFKVSFLSA...YTKKLNTQ
          |||||||| |||||||||||||  |||||  ||||| ||  ||||||||||||||||| |||||||||   ||||||||
..........PYSDELRQ.LAARLEALKENGG..LAEYH..ATEHL.TL..KAKPALEDLRQGLLPVL.SFKVSFLSA...YTKKLNTQ

Total number of restraints: 226
Potential type of restraints: undefined (226)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None
- Chain_ID: B
  None

Keywords EM, EPR, HDL, NMR, cardiovascular disease, lipoproteins, nanodisc

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 (1.285 seconds)

BMRB: 25710

Sample

Related entities 1. high-density lipoprotein particles, : 1 : 176 entities Detail

Interaction partners 1. high-density lipoprotein particles, : 37 interactors Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 7 contents Detail