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- PDB-6avo: Cryo-EM structure of human immunoproteasome with a novel noncompe... -

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Entry
Database: PDB / ID: 6avo
TitleCryo-EM structure of human immunoproteasome with a novel noncompetitive inhibitor that selectively inhibits activated lymphocytes
Descriptor(Proteasome subunit beta type- ...) x 7
(Proteasome subunit alpha type- ...) x 7
KeywordsHYDROLASE/HYDROLASE INHIBITOR / inhibitor / complex / immunoproteasome / HYDROLASE-HYDROLASE INHIBITOR complex
Specimen sourceHomo sapiens / human
MethodElectron microscopy (3.8 Å resolution / Particle / Single particle)
AuthorsLi, H. / Santos, R. / Bai, L.
CitationNat Commun, 2017, 8, 1692-1692

Nat Commun, 2017, 8, 1692-1692 Yorodumi Papers
Structure of human immunoproteasome with a reversible and noncompetitive inhibitor that selectively inhibits activated lymphocytes.
Ruda de Luna Almeida Santos / Lin Bai / Pradeep K Singh / Naoka Murakami / Hao Fan / Wenhu Zhan / Yingrong Zhu / Xiuju Jiang / Kaiming Zhang / Jean Pierre Assker / Carl F Nathan / Huilin Li / Jamil Azzi / Gang Lin

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 4, 2017 / Release: Dec 6, 2017

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Assembly

Deposited unit
A: Proteasome subunit beta type-9
B: Proteasome subunit beta type-10
C: Proteasome subunit beta type-8
D: Proteasome subunit beta type-8
E: Proteasome subunit beta type-10
F: Proteasome subunit beta type-9
G: Proteasome subunit alpha type-1
H: Proteasome subunit alpha type-5
I: Proteasome subunit alpha type-7
J: Proteasome subunit alpha type-3
K: Proteasome subunit alpha type-6
L: Proteasome subunit alpha type-1
M: Proteasome subunit alpha type-5
N: Proteasome subunit alpha type-7
O: Proteasome subunit alpha type-4
P: Proteasome subunit alpha type-2
Q: Proteasome subunit alpha type-3
R: Proteasome subunit alpha type-6
S: Proteasome subunit beta type-1
T: Proteasome subunit beta type-2
U: Proteasome subunit beta type-3
V: Proteasome subunit beta type-2
W: Proteasome subunit beta type-4
X: Proteasome subunit beta type-1
Y: Proteasome subunit beta type-3
Z: Proteasome subunit alpha type-4
a: Proteasome subunit beta type-4
b: Proteasome subunit alpha type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)716,69030
Polyers715,60528
Non-polymers1,0852
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)110300
ΔGint (kcal/M)-413
Surface area (Å2)207100

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Components

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Proteasome subunit beta type- ... , 7 types, 14 molecules AFBECDSXTV...

#1: Polypeptide(L)Proteasome subunit beta type-9 / Proteasome subunit beta type-6 / Low molecular mass protein 2 / Macropain chain 7 / Multicatalytic endopeptidase complex chain 7 / Proteasome chain 7 / Proteasome subunit beta-1i / Really interesting new gene 12 protein


Mass: 21295.000 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: P28065, EC: 3.4.25.1
#2: Polypeptide(L)Proteasome subunit beta type-10 / Proteasome subunit beta type-7 / Low molecular mass protein 10 / Macropain subunit MECl-1 / Multicatalytic endopeptidase complex subunit MECl-1 / Proteasome MECl-1 / Proteasome subunit beta-2i


Mass: 24674.248 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: P40306, EC: 3.4.25.1
#3: Polypeptide(L)Proteasome subunit beta type-8 / Proteasome subunit beta type-5 / Low molecular mass protein 7 / Macropain subunit C13 / Multicatalytic endopeptidase complex subunit C13 / Proteasome component C13 / Proteasome subunit beta-5i / Really interesting new gene 10 protein


Mass: 22685.633 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: P28062, EC: 3.4.25.1
#11: Polypeptide(L)Proteasome subunit beta type-1 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain


Mass: 23578.986 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: P20618, EC: 3.4.25.1
#12: Polypeptide(L)Proteasome subunit beta type-2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I


Mass: 22864.277 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: P49721, EC: 3.4.25.1
#13: Polypeptide(L)Proteasome subunit beta type-3 / Proteasome chain 13 / Proteasome component C10-II / Proteasome theta chain


Mass: 22972.896 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: P49720, EC: 3.4.25.1
#14: Polypeptide(L)Proteasome subunit beta type-4 / 26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome beta chain / Proteasome chain 3 / HsN3


Mass: 24414.740 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: P28070, EC: 3.4.25.1

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Proteasome subunit alpha type- ... , 7 types, 14 molecules GLHMINJQKR...

#4: Polypeptide(L)Proteasome subunit alpha type-1 / 30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / Proteasome nu chain


Mass: 29595.627 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: P25786, EC: 3.4.25.1
#5: Polypeptide(L)Proteasome subunit alpha type-5 / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


Mass: 26435.977 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: P28066, EC: 3.4.25.1
#6: Polypeptide(L)Proteasome subunit alpha type-7 / Proteasome subunit RC6-1 / Proteasome subunit XAPC7


Mass: 27929.891 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: O14818, EC: 3.4.25.1
#7: Polypeptide(L)Proteasome subunit alpha type-3 / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8


Mass: 28469.252 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: P25788, EC: 3.4.25.1
#8: Polypeptide(L)Proteasome subunit alpha type-6 / 27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


Mass: 27432.459 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: P60900, EC: 3.4.25.1
#9: Polypeptide(L)Proteasome subunit alpha type-4 / Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / Proteasome subunit L


Mass: 29525.842 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: P25789, EC: 3.4.25.1
#10: Polypeptide(L)Proteasome subunit alpha type-2 / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


Mass: 25927.535 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens / References: UniProt: P25787, EC: 3.4.25.1

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Non-polymers , 1 types, 2 molecules

#15: ChemicalChemComp-BZ7 / N~1~-{2-[([1,1'-biphenyl]-3-carbonyl)amino]ethyl}-N~4~-tert-butyl-N~2~-(3-phenylpropanoyl)-L-aspartamide / PKS21004


Mass: 542.669 Da / Num. of mol.: 2 / Formula: C32H38N4O4

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: human immunoproteasome with a novel noncompetitive inhibitor that selectively inhibits activated lymphocytes
Type: COMPLEX / Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14 / Source: NATURAL
Source (natural)Organism: Homo sapiens
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL 3200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategoryImage processing ID
4CTFFIND4CTF CORRECTION1
5GctfCTF CORRECTION1
13RELION1.4CLASSIFICATION1
14RELION1.4RECONSTRUCTION1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 75017 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00849104
ELECTRON MICROSCOPYf_angle_d0.84466591
ELECTRON MICROSCOPYf_dihedral_angle_d7.57837450
ELECTRON MICROSCOPYf_chiral_restr0.0487504
ELECTRON MICROSCOPYf_plane_restr0.0058603

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