[English] 日本語
Yorodumi
- PDB-4r67: Human constitutive 20S proteasome in complex with carfilzomib -

+
Open data


ID or keywords:

Loading...

-
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 / proteasome core complex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / immune system process / myofibril / NF-kappaB binding / proteasome endopeptidase complex ...purine ribonucleoside triphosphate binding / regulation of endopeptidase activity / proteasome core complex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / immune system process / myofibril / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / negative regulation of inflammatory response to antigenic stimulus / : / sarcomere / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / ciliary basal body / 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 / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Hh mutants are degraded by ERAD / lipopolysaccharide binding / Degradation of AXIN / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Vif-mediated degradation of APOBEC3G / Autodegradation of the E3 ubiquitin ligase COP1 / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / 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 / P-body / 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 / nuclear matrix / FCERI mediated NF-kB activation / 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 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / peptidase activity / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / regulation of inflammatory response / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / endopeptidase activity / response to oxidative stress / ficolin-1-rich granule lumen / nuclear body / ribosome / Ub-specific processing proteases / cadherin binding / intracellular membrane-bounded organelle / centrosome / ubiquitin protein ligase binding / synapse / Neutrophil degranulation / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
Components

-
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

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more