Structure of high-density lipoprotein particles
STFSKLREQL GPVTQEFWDN LEKETEGLRQ EMSKDLEEVK AKVQPYLDDF QKKWQEEMEL YRQKVEPLGE EMRDRARAHV DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ GLLPVLESFK VSFLSALEEY TKKLNTQ
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 TKKLNTQSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 316 K, pH 7.4
# | Name | Isotope labeling | Type | 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 |
Bruker Avance - 900 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 316 K, pH 7.4
# | Name | Isotope labeling | Type | 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 |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 316 K, pH 7.4
# | Name | Isotope labeling | Type | 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 |
Bruker Avance - 700 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 316 K, pH 7.4
# | Name | Isotope labeling | Type | 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 |
Bruker Avance - 700 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 316 K, pH 7.4
# | Name | Isotope labeling | Type | 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 |
Bruker Avance - 900 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 316 K, pH 7.4
# | Name | Isotope labeling | Type | 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 |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 316 K, pH 7.4
# | Name | Isotope labeling | Type | 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 |
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
NoneOther bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
NoneNon-standard residues
NoneSequence alignments
----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-------
----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
Assigned chemical shifts
----60--------70--------80--------90-------100-------110-------120-------130-------140-------150---- ..FSKLREQLGPVTQEFWDNLEKETEGLRQEMSKDLEEVKAK..PYLDDFQKKWQEEMELYRQ.VE......................PLGEEMRDRARA |||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||| || |||||||||||| ..FSKLREQLGPVTQEFWDNLEKETEGLRQEMSKDLEEVKAK..PYLDDFQKKWQEEMELYRQ.VE......................PLGEEMRDRARA ---160-------170-------180-------190-------200-------210-------220-------230-------240--- HVDALRTHLAPYSDELRQRLAARLEALKENGGARLAEYHAKATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALEEYTKKLNTQ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| HVDALRTHLAPYSDELRQRLAARLEALKENGGARLAEYHAKATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALEEYTKKLNTQ
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
----60--------70--------80--------90-------100-------110-------120-------130-------140-------150---- ...SKLREQLG.VTQE.WDN.EKE.EG.R.EMSKD....KAK...YLDDF.K..Q.EMELYRQ..................................... |||||||| |||| ||| ||| || | ||||| ||| ||||| | | ||||||| ...SKLREQLG.VTQE.WDN.EKE.EG.R.EMSKD....KAK...YLDDF.K..Q.EMELYRQ..................................... ---160-------170-------180-------190-------200-------210-------220-------230-------240--- ...........YSDELR.RLAA.LEA.KENG..RL.E..AKAT.HLSTL.EKAK.A.ED.RQGLL.VLE..KVS.L.AL.E.TKKLN.Q |||||| |||| ||| |||| || | |||| ||||| |||| | || ||||| ||| ||| | || | ||||| | ...........YSDELR.RLAA.LEA.KENG..RL.E..AKAT.HLSTL.EKAK.A.ED.RQGLL.VLE..KVS.L.AL.E.TKKLN.Q
----60--------70--------80--------90-------100-------110-------120-------130-------140-------150---- ..F.KLREQLG.VTQEFWDNLEKE..GL...MSKDLE.VKAKV..YLDDFQKKWQ.EMELYRQ.VE.................................. | ||||||| |||||||||||| || |||||| ||||| |||||||||| ||||||| || ..F.KLREQLG.VTQEFWDNLEKE..GL...MSKDLE.VKAKV..YLDDFQKKWQ.EMELYRQ.VE.................................. ---160-------170-------180-------190-------200-------210-------220-------230-------240--- ...........YSDELRQRLAARLEALKENGG.RLA.YHAKATEHLSTLS.KAK.ALEDLRQGLL.VLE.FKVSFL.AL....KKLN.Q ||||||||||||||||||||| ||| ||||||||||||| ||| |||||||||| ||| |||||| || |||| | ...........YSDELRQRLAARLEALKENGG.RLA.YHAKATEHLSTLS.KAK.ALEDLRQGLL.VLE.FKVSFL.AL....KKLN.Q
----60--------70--------80--------90-------100-------110-------120-------130-------140-------150---- ..F.KLREQLG.VTQEFWDNLEKE..GL...MSKDLE.VKAKV..YLDDFQKKWQ.EMELYRQ.VE.................................. | ||||||| |||||||||||| || |||||| ||||| |||||||||| ||||||| || ..F.KLREQLG.VTQEFWDNLEKE..GL...MSKDLE.VKAKV..YLDDFQKKWQ.EMELYRQ.VE.................................. ---160-------170-------180-------190-------200-------210-------220-------230-------240--- ...........YSDELRQRLAARLEALKENGG.RLA.YHAKATEHLSTL..KAK.ALEDLRQGLL.VLE.FKVSFL.AL....KKLN.Q ||||||||||||||||||||| ||| |||||||||||| ||| |||||||||| ||| |||||| || |||| | ...........YSDELRQRLAARLEALKENGG.RLA.YHAKATEHLSTL..KAK.ALEDLRQGLL.VLE.FKVSFL.AL....KKLN.Q
----60--------70--------80--------90-------100-------110-------120-------130-------140-------150---- ...SK..EQ...VTQEFWDNLEKE..GLRQEMSKDLEEVKAKVQPYLDDFQKKWQEEMELYRQKVE.................................. || || |||||||||||| |||||||||||||||||||||||||||||||||||||||| ...SK..EQ...VTQEFWDNLEKE..GLRQEMSKDLEEVKAKVQPYLDDFQKKWQEEMELYRQKVE.................................. ---160-------170-------180-------190-------200-------210-------220-------230-------240--- ...........YSDELRQRLAARLEALKENGGARLAEYHAKATEHLSTLSE...PALEDLRQGLLPVLESFKVSFL.ALE.YTKKLN.Q |||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| ||| |||||| | ...........YSDELRQRLAARLEALKENGGARLAEYHAKATEHLSTLSE...PALEDLRQGLLPVLESFKVSFL.ALE.YTKKLN.Q
----60--------70--------80--------90-------100-------110-------120-------130-------140-------150---- ...SK..EQ...VTQEFWDNLEKE..GLRQEMSKDLEEVKAKVQPYLDDFQKKWQEEMELYRQKVE.................................. || || |||||||||||| |||||||||||||||||||||||||||||||||||||||| ...SK..EQ...VTQEFWDNLEKE..GLRQEMSKDLEEVKAKVQPYLDDFQKKWQEEMELYRQKVE.................................. ---160-------170-------180-------190-------200-------210-------220-------230-------240--- ...........YSDELRQRLAARLEALKENGGARLAEYHAKATEHLSTLSE...PALEDLRQGLLPVLESFKVSFL.ALEEYTKKLN.Q |||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||| | ...........YSDELRQRLAARLEALKENGGARLAEYHAKATEHLSTLSE...PALEDLRQGLLPVLESFKVSFL.ALEEYTKKLN.Q
Dihedral angle restraints
----60--------70--------80--------90-------100-------110-------120-------130-------140-------150---- ..FSKLREQLGPVTQEFWDNLEKETEGLRQEMSKDLEEVKAKV.PYLDDFQKKWQEEMELYRQKVE......................P........... ||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| | ..FSKLREQLGPVTQEFWDNLEKETEGLRQEMSKDLEEVKAKV.PYLDDFQKKWQEEMELYRQKVE......................P........... ---160-------170-------180-------190-------200-------210-------220-------230-------240--- ............SDELRQRLAARLEALKENGGARLAEYHAKATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALEEYTKKLNTQ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ............SDELRQRLAARLEALKENGGARLAEYHAKATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALEEYTKKLNTQ
----60--------70--------80--------90-------100-------110-------120-------130-------140-------150---- ..FSKLREQLGPVTQEFWDNLEKETEGLRQEMSKDLEEVKAKV.PYLDDFQKKWQEEMELYRQKVE......................P........... ||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| | ..FSKLREQLGPVTQEFWDNLEKETEGLRQEMSKDLEEVKAKV.PYLDDFQKKWQEEMELYRQKVE......................P........... ---160-------170-------180-------190-------200-------210-------220-------230-------240--- ............SDELRQRLAARLEALKENGGARLAEYHAKATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALEEYTKKLNTQ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ............SDELRQRLAARLEALKENGGARLAEYHAKATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALEEYTKKLNTQ
RDC restraints
----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
----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