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- PDB-4r67: Human constitutive 20S proteasome in complex with carfilzomib -

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Basic information

Entry
Database: PDB / ID: 4r67
TitleHuman constitutive 20S proteasome in complex with carfilzomib
Components
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


purine ribonucleoside triphosphate binding / regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / : / Somitogenesis / myofibril / immune system process / NF-kappaB binding ...purine ribonucleoside triphosphate binding / regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / : / Somitogenesis / myofibril / immune system process / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / sarcomere / proteasome complex / ciliary basal body / Regulation of activated PAK-2p34 by proteasome mediated degradation / proteolysis involved in protein catabolic process / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Degradation of DVL / negative regulation of inflammatory response to antigenic stimulus / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / lipopolysaccharide binding / Hh mutants are degraded by ERAD / Degradation of AXIN / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / G2/M Checkpoints / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / P-body / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / response to virus / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / response to organic cyclic compound / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / nuclear matrix / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / peptidase activity / positive regulation of NF-kappaB transcription factor activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / regulation of inflammatory response / secretory granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / ficolin-1-rich granule lumen / postsynapse / response to oxidative stress / nuclear body / Ub-specific processing proteases / ribosome / cadherin binding / intracellular membrane-bounded organelle / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / synapse / mitochondrion / proteolysis / RNA binding
Similarity search - Function
Proteasome subunit alpha 1 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 ...Proteasome subunit alpha 1 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CARFILZOMIB, bound form / Chem-3BV / Proteasome subunit alpha type-7 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 ...CARFILZOMIB, bound form / Chem-3BV / Proteasome subunit alpha type-7 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / Proteasome subunit alpha type-6 / Proteasome subunit beta type-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsSacchettini, J.C. / Harshbarger, W.H.
CitationJournal: Structure / Year: 2015
Title: Crystal Structure of the Human 20S Proteasome in Complex with Carfilzomib.
Authors: Harshbarger, W. / Miller, C. / Diedrich, C. / Sacchettini, J.
History
DepositionAug 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome subunit alpha type-6
B: Proteasome subunit alpha type-2
C: Proteasome subunit alpha type-4
D: Proteasome subunit alpha type-7
E: Proteasome subunit alpha type-5
F: Proteasome subunit alpha type-1
G: Proteasome subunit alpha type-3
H: Proteasome subunit beta type-6
I: Proteasome subunit beta type-7
J: Proteasome subunit beta type-3
K: Proteasome subunit beta type-2
L: Proteasome subunit beta type-5
M: Proteasome subunit beta type-1
N: Proteasome subunit beta type-4
O: Proteasome subunit alpha type-6
P: Proteasome subunit alpha type-2
Q: Proteasome subunit alpha type-4
R: Proteasome subunit alpha type-7
S: Proteasome subunit alpha type-5
T: Proteasome subunit alpha type-1
U: Proteasome subunit alpha type-3
V: Proteasome subunit beta type-6
W: Proteasome subunit beta type-7
X: Proteasome subunit beta type-3
Y: Proteasome subunit beta type-2
Z: Proteasome subunit beta type-5
1: Proteasome subunit beta type-1
2: Proteasome subunit beta type-4
c: Proteasome subunit alpha type-6
d: Proteasome subunit alpha type-2
e: Proteasome subunit alpha type-4
f: Proteasome subunit alpha type-7
g: Proteasome subunit alpha type-5
h: Proteasome subunit alpha type-1
i: Proteasome subunit alpha type-3
j: Proteasome subunit beta type-6
k: Proteasome subunit beta type-7
l: Proteasome subunit beta type-3
m: Proteasome subunit beta type-2
n: Proteasome subunit beta type-5
o: Proteasome subunit beta type-1
p: Proteasome subunit beta type-4
q: Proteasome subunit alpha type-6
r: Proteasome subunit alpha type-2
s: Proteasome subunit alpha type-4
t: Proteasome subunit alpha type-7
u: Proteasome subunit alpha type-5
v: Proteasome subunit alpha type-1
w: Proteasome subunit alpha type-3
x: Proteasome subunit beta type-6
y: Proteasome subunit beta type-7
z: Proteasome subunit beta type-3
0: Proteasome subunit beta type-2
3: Proteasome subunit beta type-5
a: Proteasome subunit beta type-1
b: Proteasome subunit beta type-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,403,75767
Polymers1,395,79456
Non-polymers7,96311
Water3,927218
1
A: Proteasome subunit alpha type-6
B: Proteasome subunit alpha type-2
C: Proteasome subunit alpha type-4
D: Proteasome subunit alpha type-7
E: Proteasome subunit alpha type-5
F: Proteasome subunit alpha type-1
G: Proteasome subunit alpha type-3
H: Proteasome subunit beta type-6
I: Proteasome subunit beta type-7
J: Proteasome subunit beta type-3
K: Proteasome subunit beta type-2
L: Proteasome subunit beta type-5
M: Proteasome subunit beta type-1
N: Proteasome subunit beta type-4
O: Proteasome subunit alpha type-6
P: Proteasome subunit alpha type-2
Q: Proteasome subunit alpha type-4
R: Proteasome subunit alpha type-7
S: Proteasome subunit alpha type-5
T: Proteasome subunit alpha type-1
U: Proteasome subunit alpha type-3
V: Proteasome subunit beta type-6
W: Proteasome subunit beta type-7
X: Proteasome subunit beta type-3
Y: Proteasome subunit beta type-2
Z: Proteasome subunit beta type-5
1: Proteasome subunit beta type-1
2: Proteasome subunit beta type-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)702,24134
Polymers697,89728
Non-polymers4,3446
Water59433
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area112130 Å2
ΔGint-370 kcal/mol
Surface area213180 Å2
MethodPISA
2
c: Proteasome subunit alpha type-6
d: Proteasome subunit alpha type-2
e: Proteasome subunit alpha type-4
f: Proteasome subunit alpha type-7
g: Proteasome subunit alpha type-5
h: Proteasome subunit alpha type-1
i: Proteasome subunit alpha type-3
j: Proteasome subunit beta type-6
k: Proteasome subunit beta type-7
l: Proteasome subunit beta type-3
m: Proteasome subunit beta type-2
n: Proteasome subunit beta type-5
o: Proteasome subunit beta type-1
p: Proteasome subunit beta type-4
q: Proteasome subunit alpha type-6
r: Proteasome subunit alpha type-2
s: Proteasome subunit alpha type-4
t: Proteasome subunit alpha type-7
u: Proteasome subunit alpha type-5
v: Proteasome subunit alpha type-1
w: Proteasome subunit alpha type-3
x: Proteasome subunit beta type-6
y: Proteasome subunit beta type-7
z: Proteasome subunit beta type-3
0: Proteasome subunit beta type-2
3: Proteasome subunit beta type-5
a: Proteasome subunit beta type-1
b: Proteasome subunit beta type-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)701,51733
Polymers697,89728
Non-polymers3,6205
Water54030
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area112190 Å2
ΔGint-372 kcal/mol
Surface area213160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.989, 201.027, 225.585
Angle α, β, γ (deg.)90.00, 107.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42
13
23
33
43
14
24
34
44
15
25
35
45
16
26
36
46
17
27
37
47
18
28
38
48
19
29
39
49
110
210
310
410
111
211
311
411
112
212
312
412
113
213
313
413
114
214
314
414

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'C' and (resseq 2:251 )
211chain 'Q' and (resseq 2:251 )
311chain 'e' and (resseq 2:251 )
411chain 's' and (resseq 2:251 )
112chain 'G' and (resseq 2:245 )
212chain 'U' and (resseq 2:245 )
312chain 'i' and (resseq 2:245 )
412chain 'w' and (resseq 2:245 )
113chain 'A' and (resseq 2:245 )
213chain 'O' and (resseq 2:245 )
313chain 'c' and (resseq 2:245 )
413chain 'q' and (resseq 2:245 )
114chain 'D' and (resseq 2:244 )
214chain 'R' and (resseq 2:244 )
314chain 'f' and (resseq 2:244 )
414chain 't' and (resseq 2:244 )
115chain 'F' and (resseq 4:239 )
215chain 'T' and (resseq 4:239 )
315chain 'h' and (resseq 4:239 )
415chain 'v' and (resseq 4:239 )
116chain 'E' and (resseq 8:241 )
216chain 'S' and (resseq 8:241 )
316chain 'g' and (resseq 8:241 )
416chain 'u' and (resseq 8:241 )
117chain 'B' and (resseq 1:51 or resseq 53:233 )
217chain 'P' and (resseq 1:51 or resseq 53:233 )
317chain 'd' and (resseq 1:51 or resseq 53:233 )
417chain 'r' and (resseq 1:51 or resseq 53:233 )
118chain 'I' and (resseq 1:220 )
218chain 'W' and (resseq 1:220 )
318chain 'k' and (resseq 1:220 )
418chain 'y' and (resseq 1:220 )
119chain 'N' and (resseq 1:217 )
219chain '2' and (resseq 1:217 )
319chain 'p' and (resseq 1:217 )
419chain 'b' and (resseq 1:217 )
1110chain 'M' and (resseq 1:213 )
2110chain '1' and (resseq 1:213 )
3110chain 'o' and (resseq 1:213 )
4110chain 'a' and (resseq 1:213 )
1111chain 'J' and (resseq 2:205 )
2111chain 'X' and (resseq 2:205 )
3111chain 'l' and (resseq 2:205 )
4111chain 'z' and (resseq 2:205 )
1112chain 'H' and (resseq 1:202 )
2112chain 'V' and (resseq 1:202 )
3112chain 'j' and (resseq 1:202 )
4112chain 'x' and (resseq 1:202 )
1113chain 'L' and (resseq 1:201 )
2113chain 'Z' and (resseq 1:201 )
3113chain 'n' and (resseq 1:201 )
4113chain '3' and (resseq 1:201 )
1114chain 'K' and (resseq 1:199 )
2114chain 'Y' and (resseq 1:199 )
3114chain 'm' and (resseq 1:199 )
4114chain '0' and (resseq 1:199 )

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
Details20S Eukaryotic Proteasomes have C2 symmetry with 28 total subunits, 14 being unique.

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Components

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Proteasome subunit alpha type- ... , 7 types, 28 molecules AOcqBPdrCQesDRftESguFThvGUiw

#1: Protein
Proteasome subunit alpha type-6 / 27 kDa prosomal protein / PROS-27 / p27K / Macropain iota chain / Multicatalytic endopeptidase ...27 kDa prosomal protein / PROS-27 / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


Mass: 27186.174 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: red blood cells
References: UniProt: P60900, proteasome endopeptidase complex
#2: Protein
Proteasome subunit alpha type-2 / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


Mass: 25796.338 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: red blood cells
References: UniProt: P25787, proteasome endopeptidase complex
#3: Protein
Proteasome subunit alpha type-4 / Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / ...Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / Proteasome subunit L


Mass: 28118.189 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 2-251 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: red blood cells
References: UniProt: P25789, proteasome endopeptidase complex
#4: Protein
Proteasome subunit alpha type-7 / Proteasome subunit RC6-1 / Proteasome subunit XAPC7


Mass: 27382.178 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 2-244 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: red blood cells
References: UniProt: O14818, proteasome endopeptidase complex
#5: Protein
Proteasome subunit alpha type-5 / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


Mass: 25569.957 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 8-241 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: red blood cells
References: UniProt: P28066, proteasome endopeptidase complex
#6: Protein
Proteasome subunit alpha type-1 / 30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex ...30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / Proteasome nu chain


Mass: 26728.428 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 4-241 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: red blood cells
References: UniProt: P25786, proteasome endopeptidase complex
#7: Protein
Proteasome subunit alpha type-3 / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8


Mass: 27287.100 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 2-246 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: red blood cells
References: UniProt: P25788, proteasome endopeptidase complex

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Proteasome subunit beta type- ... , 7 types, 28 molecules HVjxIWkyJXlzKYm0LZn3M1oaN2pb

#8: Protein
Proteasome subunit beta type-6 / Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / ...Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / Proteasome subunit Y


Mass: 21656.527 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 35-236 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: red blood cells
References: UniProt: P28072, proteasome endopeptidase complex
#9: Protein
Proteasome subunit beta type-7 / Macropain chain Z / Multicatalytic endopeptidase complex chain Z / Proteasome subunit Z


Mass: 23745.256 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 44-263 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: red blood cells
References: UniProt: Q99436, proteasome endopeptidase complex
#10: Protein
Proteasome subunit beta type-3 / Proteasome chain 13 / Proteasome component C10-II / Proteasome theta chain


Mass: 22841.701 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: red blood cells
References: UniProt: P49720, proteasome endopeptidase complex
#11: Protein
Proteasome subunit beta type-2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I


Mass: 22720.146 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 1-199 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: red blood cells
References: UniProt: P49721, proteasome endopeptidase complex
#12: Protein
Proteasome subunit beta type-5 / Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / ...Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / Proteasome epsilon chain / Proteasome subunit MB1 / Proteasome subunit X


Mass: 22199.072 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 60-260 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: red blood cells
References: UniProt: P28074, proteasome endopeptidase complex
#13: Protein
Proteasome subunit beta type-1 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / ...Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain


Mass: 23578.986 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 29-241 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: red blood cells
References: UniProt: P20618, proteasome endopeptidase complex
#14: Protein
Proteasome subunit beta type-4 / 26 kDa prosomal protein / HsBPROS26 / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase ...26 kDa prosomal protein / HsBPROS26 / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome beta chain / Proteasome chain 3 / HsN3


Mass: 24138.453 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 46-262 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: red blood cells
References: UniProt: P28070, proteasome endopeptidase complex

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Non-polymers , 2 types, 229 molecules

#15: Chemical
ChemComp-3BV / N-{(2S)-2-[(morpholin-4-ylacetyl)amino]-4-phenylbutanoyl}-L-leucyl-N-[(2R,3S,4S)-1,3-dihydroxy-2,6-dimethylheptan-4-yl]-L-phenylalaninamide / CARFILZOMIB, bound form


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 723.942 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C40H61N5O7 / References: CARFILZOMIB, bound form / Comment: medication, anticancer, inhibitor*YM
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.2M sodium formate, 40% MPD, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. all: 321261 / Num. obs: 320820 / % possible obs: 98.7 % / Redundancy: 3.7 %
Reflection shellResolution: 2.89→2.99 Å / Redundancy: 3.4 % / % possible all: 91.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHENIX(Phaser-MR)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→33.505 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 29.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2451 16188 5.05 %
Rwork0.2151 --
obs0.2166 320820 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.89→33.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms95215 0 572 218 96005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00397513
X-RAY DIFFRACTIONf_angle_d0.712132088
X-RAY DIFFRACTIONf_dihedral_angle_d12.76135113
X-RAY DIFFRACTIONf_chiral_restr0.0514976
X-RAY DIFFRACTIONf_plane_restr0.00317139
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C1902X-RAY DIFFRACTIONPOSITIONAL
12Q1902X-RAY DIFFRACTIONPOSITIONAL0.008
13E1902X-RAY DIFFRACTIONPOSITIONAL0.007
14S1902X-RAY DIFFRACTIONPOSITIONAL0.007
21G1879X-RAY DIFFRACTIONPOSITIONAL
22U1879X-RAY DIFFRACTIONPOSITIONAL0.009
23I1879X-RAY DIFFRACTIONPOSITIONAL0.009
24W1879X-RAY DIFFRACTIONPOSITIONAL0.009
31A1842X-RAY DIFFRACTIONPOSITIONAL
32O1842X-RAY DIFFRACTIONPOSITIONAL0.007
33C1842X-RAY DIFFRACTIONPOSITIONAL0.006
34Q1842X-RAY DIFFRACTIONPOSITIONAL0.007
41D1675X-RAY DIFFRACTIONPOSITIONAL
42R1675X-RAY DIFFRACTIONPOSITIONAL0.007
43F1668X-RAY DIFFRACTIONPOSITIONAL0.006
44T1672X-RAY DIFFRACTIONPOSITIONAL0.006
51F1838X-RAY DIFFRACTIONPOSITIONAL
52T1838X-RAY DIFFRACTIONPOSITIONAL0.036
53H1838X-RAY DIFFRACTIONPOSITIONAL0.011
54V1838X-RAY DIFFRACTIONPOSITIONAL0.031
61E1759X-RAY DIFFRACTIONPOSITIONAL
62S1759X-RAY DIFFRACTIONPOSITIONAL0.007
63G1759X-RAY DIFFRACTIONPOSITIONAL0.006
64U1759X-RAY DIFFRACTIONPOSITIONAL0.006
71B1702X-RAY DIFFRACTIONPOSITIONAL
72P1702X-RAY DIFFRACTIONPOSITIONAL0.068
73D1702X-RAY DIFFRACTIONPOSITIONAL0.013
74R1702X-RAY DIFFRACTIONPOSITIONAL0.068
81I1643X-RAY DIFFRACTIONPOSITIONAL
82W1643X-RAY DIFFRACTIONPOSITIONAL0.009
83K1643X-RAY DIFFRACTIONPOSITIONAL0.008
84Y1643X-RAY DIFFRACTIONPOSITIONAL0.008
91N1672X-RAY DIFFRACTIONPOSITIONAL
9221672X-RAY DIFFRACTIONPOSITIONAL0.009
93P1672X-RAY DIFFRACTIONPOSITIONAL0.008
94B1669X-RAY DIFFRACTIONPOSITIONAL0.008
101M1639X-RAY DIFFRACTIONPOSITIONAL
10211639X-RAY DIFFRACTIONPOSITIONAL0.026
103O1639X-RAY DIFFRACTIONPOSITIONAL0.01
104A1639X-RAY DIFFRACTIONPOSITIONAL0.012
111J1585X-RAY DIFFRACTIONPOSITIONAL
112X1585X-RAY DIFFRACTIONPOSITIONAL0.065
113L1585X-RAY DIFFRACTIONPOSITIONAL0.065
114Z1585X-RAY DIFFRACTIONPOSITIONAL0.065
121H1509X-RAY DIFFRACTIONPOSITIONAL
122V1509X-RAY DIFFRACTIONPOSITIONAL0.008
123J1509X-RAY DIFFRACTIONPOSITIONAL0.007
124X1509X-RAY DIFFRACTIONPOSITIONAL0.008
131L1548X-RAY DIFFRACTIONPOSITIONAL
132Z1548X-RAY DIFFRACTIONPOSITIONAL0.033
133N1548X-RAY DIFFRACTIONPOSITIONAL0.008
13431548X-RAY DIFFRACTIONPOSITIONAL0.008
141K1570X-RAY DIFFRACTIONPOSITIONAL
142Y1570X-RAY DIFFRACTIONPOSITIONAL0.008
143M1570X-RAY DIFFRACTIONPOSITIONAL0.008
14401570X-RAY DIFFRACTIONPOSITIONAL0.008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.92210.41314710.36278367X-RAY DIFFRACTION82
2.9221-2.95650.39144880.35619968X-RAY DIFFRACTION96
2.9565-2.99250.36345720.33539869X-RAY DIFFRACTION97
2.9925-3.03040.35955050.333510013X-RAY DIFFRACTION97
3.0304-3.07020.3775160.32910068X-RAY DIFFRACTION98
3.0702-3.11230.35825210.327810201X-RAY DIFFRACTION98
3.1123-3.15670.33245150.304710044X-RAY DIFFRACTION99
3.1567-3.20380.31535600.289210177X-RAY DIFFRACTION99
3.2038-3.25380.30895450.282910249X-RAY DIFFRACTION99
3.2538-3.30710.31655770.278810210X-RAY DIFFRACTION100
3.3071-3.36410.31265550.262410174X-RAY DIFFRACTION99
3.3641-3.42520.26785800.245710221X-RAY DIFFRACTION100
3.4252-3.4910.29065640.241110195X-RAY DIFFRACTION100
3.491-3.56220.26525210.237110291X-RAY DIFFRACTION100
3.5622-3.63950.26395360.228410311X-RAY DIFFRACTION100
3.6395-3.72410.2615030.233810337X-RAY DIFFRACTION100
3.7241-3.81710.2755760.229310190X-RAY DIFFRACTION100
3.8171-3.92020.24025440.216910305X-RAY DIFFRACTION100
3.9202-4.03530.24555430.20910287X-RAY DIFFRACTION100
4.0353-4.16530.23055460.197710265X-RAY DIFFRACTION100
4.1653-4.31390.22645440.186110302X-RAY DIFFRACTION100
4.3139-4.48630.20285540.17810294X-RAY DIFFRACTION100
4.4863-4.68990.19745530.174210287X-RAY DIFFRACTION100
4.6899-4.93650.20735690.175210253X-RAY DIFFRACTION100
4.9365-5.24470.22715310.190510325X-RAY DIFFRACTION100
5.2447-5.64780.25245390.214210342X-RAY DIFFRACTION100
5.6478-6.21290.24115670.215510317X-RAY DIFFRACTION100
6.2129-7.10450.23445310.204810355X-RAY DIFFRACTION100
7.1045-8.92280.17425680.153610358X-RAY DIFFRACTION100
8.9228-33.50710.17784940.165910057X-RAY DIFFRACTION95

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