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- PDB-6ey2: Crystal structure of XIAP-BIR3 in complex with a cIAP1-selective SM -

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Basic information

Entry
Database: PDB / ID: 6ey2
TitleCrystal structure of XIAP-BIR3 in complex with a cIAP1-selective SM
ComponentsE3 ubiquitin-protein ligase XIAP
KeywordsSIGNALING PROTEIN / Zinc finger motif / smac-mimetic / protein-ligand complex / BIR domain
Function / homology
Function and homology information


regulation of apoptosis involved in tissue homeostasis / positive regulation of protein linear polyubiquitination / copper ion homeostasis / regulation of BMP signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Activation of caspases through apoptosome-mediated cleavage ...regulation of apoptosis involved in tissue homeostasis / positive regulation of protein linear polyubiquitination / copper ion homeostasis / regulation of BMP signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / regulation of innate immune response / cysteine-type endopeptidase inhibitor activity / protein K63-linked ubiquitination / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of type I interferon production / protein serine/threonine kinase binding / Regulation of PTEN localization / positive regulation of protein ubiquitination / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of JNK cascade / Deactivation of the beta-catenin transactivating complex / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / Regulation of necroptotic cell death / Wnt signaling pathway / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / regulation of inflammatory response / neuron apoptotic process / regulation of apoptotic process / response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / regulation of cell cycle / defense response to bacterium / DNA damage response / negative regulation of apoptotic process / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
XIAP/BIRC8, UBA domain / : / BIRC2/3-like, UBA domain / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / : / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. ...XIAP/BIRC8, UBA domain / : / BIRC2/3-like, UBA domain / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / : / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Zinc finger, C3HC4 type (RING finger) / Death-like domain superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-C3T / E3 ubiquitin-protein ligase XIAP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCossu, F. / Corti, A. / Milani, M. / Mastrangelo, E.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchAIRC MFAG 17083 Italy
CitationJournal: FEBS J. / Year: 2018
Title: Structure-based design and molecular profiling of Smac-mimetics selective for cellular IAPs.
Authors: Corti, A. / Milani, M. / Lecis, D. / Seneci, P. / de Rosa, M. / Mastrangelo, E. / Cossu, F.
History
DepositionNov 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase XIAP
B: E3 ubiquitin-protein ligase XIAP
C: E3 ubiquitin-protein ligase XIAP
D: E3 ubiquitin-protein ligase XIAP
E: E3 ubiquitin-protein ligase XIAP
F: E3 ubiquitin-protein ligase XIAP
G: E3 ubiquitin-protein ligase XIAP
H: E3 ubiquitin-protein ligase XIAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,29124
Polymers131,8748
Non-polymers4,41616
Water1,53185
1
A: E3 ubiquitin-protein ligase XIAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0363
Polymers16,4841
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase XIAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0363
Polymers16,4841
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: E3 ubiquitin-protein ligase XIAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0363
Polymers16,4841
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: E3 ubiquitin-protein ligase XIAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0363
Polymers16,4841
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: E3 ubiquitin-protein ligase XIAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0363
Polymers16,4841
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: E3 ubiquitin-protein ligase XIAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0363
Polymers16,4841
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: E3 ubiquitin-protein ligase XIAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0363
Polymers16,4841
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: E3 ubiquitin-protein ligase XIAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0363
Polymers16,4841
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.230, 97.060, 182.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUAA254 - 35044 - 140
21GLUGLUBB254 - 35044 - 140
12LEULEUAA254 - 35244 - 142
22LEULEUCC254 - 35244 - 142
13CYSCYSAA254 - 35144 - 141
23CYSCYSDD254 - 35144 - 141
14CYSCYSAA254 - 35144 - 141
24CYSCYSEE254 - 35144 - 141
15CYSCYSAA254 - 35144 - 141
25CYSCYSFF254 - 35144 - 141
16CYSCYSAA254 - 35144 - 141
26CYSCYSGG254 - 35144 - 141
17LEULEUAA254 - 35244 - 142
27LEULEUHH254 - 35244 - 142
18GLUGLUBB254 - 35044 - 140
28GLUGLUCC254 - 35044 - 140
19GLUGLUBB254 - 35044 - 140
29GLUGLUDD254 - 35044 - 140
110GLUGLUBB254 - 35044 - 140
210GLUGLUEE254 - 35044 - 140
111GLUGLUBB254 - 35044 - 140
211GLUGLUFF254 - 35044 - 140
112GLUGLUBB254 - 35044 - 140
212GLUGLUGG254 - 35044 - 140
113GLUGLUBB254 - 35044 - 140
213GLUGLUHH254 - 35044 - 140
114CYSCYSCC254 - 35144 - 141
214CYSCYSDD254 - 35144 - 141
115CYSCYSCC254 - 35144 - 141
215CYSCYSEE254 - 35144 - 141
116CYSCYSCC254 - 35144 - 141
216CYSCYSFF254 - 35144 - 141
117CYSCYSCC254 - 35144 - 141
217CYSCYSGG254 - 35144 - 141
118LEULEUCC254 - 35244 - 142
218LEULEUHH254 - 35244 - 142
119CYSCYSDD254 - 35144 - 141
219CYSCYSEE254 - 35144 - 141
120ARGARGDD254 - 35444 - 144
220ARGARGFF254 - 35444 - 144
121LEULEUDD254 - 35244 - 142
221LEULEUGG254 - 35244 - 142
122CYSCYSDD254 - 35144 - 141
222CYSCYSHH254 - 35144 - 141
123CYSCYSEE254 - 35144 - 141
223CYSCYSFF254 - 35144 - 141
124CYSCYSEE254 - 35144 - 141
224CYSCYSGG254 - 35144 - 141
125CYSCYSEE254 - 35144 - 141
225CYSCYSHH254 - 35144 - 141
126LEULEUFF254 - 35244 - 142
226LEULEUGG254 - 35244 - 142
127CYSCYSFF254 - 35144 - 141
227CYSCYSHH254 - 35144 - 141
128CYSCYSGG254 - 35144 - 141
228CYSCYSHH254 - 35144 - 141

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
E3 ubiquitin-protein ligase XIAP / Baculoviral IAP repeat-containing protein 4 / IAP-like protein / hILP / Inhibitor of apoptosis ...Baculoviral IAP repeat-containing protein 4 / IAP-like protein / hILP / Inhibitor of apoptosis protein 3 / hIAP3 / RING-type E3 ubiquitin transferase XIAP / X-linked inhibitor of apoptosis protein / X-linked IAP


Mass: 16484.309 Da / Num. of mol.: 8 / Fragment: Zinc-finger protein / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XIAP, API3, BIRC4, IAP3 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P98170, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Fragment: SM / Mutation: none / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-C3T / (3~{S},6~{S},7~{S},9~{a}~{S})-~{N}-[(4-~{tert}-butylphenyl)methyl]-7-(hydroxymethyl)-6-[[(2~{S})-2-(methylamino)butanoyl]amino]-5-oxidanylidene-1,2,3,6,7,8,9,9~{a}-octahydropyrrolo[1,2-a]azepine-3-carboxamide


Mass: 486.647 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C27H42N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5 / Details: 10% PEG 400, 0.2 M MgCl2, 0.1M Hepes-Na

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 16, 2012 / Details: Toroidal focusing mirror
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.7→66.5 Å / Num. obs: 28799 / % possible obs: 100 % / Redundancy: 6 % / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.136 / Net I/σ(I): 8
Reflection shellResolution: 2.7→2.85 Å / Rmerge(I) obs: 0.718 / Num. measured obs: 25715 / Num. unique all: 4113 / Rrim(I) all: 0.78

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
SCALAdata scaling
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CLX

3clx


Resolution: 2.7→66.5 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.897 / SU B: 17.896 / SU ML: 0.357 / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28408 1440 5 %RANDOM
Rwork0.2351 ---
obs0.23761 27239 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.01 Å2
Baniso -1Baniso -2Baniso -3
1-4.29 Å20 Å20 Å2
2--2 Å20 Å2
3----6.29 Å2
Refinement stepCycle: 1 / Resolution: 2.7→66.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6485 0 288 85 6858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0147025
X-RAY DIFFRACTIONr_bond_other_d0.0050.0186039
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.7089554
X-RAY DIFFRACTIONr_angle_other_deg1.2491.73314181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1295797
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08423.432373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.091151082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6561525
X-RAY DIFFRACTIONr_chiral_restr0.0780.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027796
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021438
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.4667.0183212
X-RAY DIFFRACTIONr_mcbond_other6.4637.0183212
X-RAY DIFFRACTIONr_mcangle_it9.85410.4953989
X-RAY DIFFRACTIONr_mcangle_other9.85410.4973990
X-RAY DIFFRACTIONr_scbond_it6.2497.4963813
X-RAY DIFFRACTIONr_scbond_other6.2487.4973814
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.71111.1145562
X-RAY DIFFRACTIONr_long_range_B_refined13.36479.6278239
X-RAY DIFFRACTIONr_long_range_B_other13.36379.6348240
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A30970.1
12B30970.1
21A31960.1
22C31960.1
31A31890.09
32D31890.09
41A31560.09
42E31560.09
51A31280.1
52F31280.1
61A31570.09
62G31570.09
71A32210.08
72H32210.08
81B31050.1
82C31050.1
91B31700.09
92D31700.09
101B31430.09
102E31430.09
111B31060.1
112F31060.1
121B31650.09
122G31650.09
131B31740.08
132H31740.08
141C32000.09
142D32000.09
151C32030.08
152E32030.08
161C31630.1
162F31630.1
171C32110.1
172G32110.1
181C32150.09
182H32150.09
191D32360.08
192E32360.08
201D32960.08
202F32960.08
211D32830.07
212G32830.07
221D32640.07
222H32640.07
231E31950.08
232F31950.08
241E32300.08
242G32300.08
251E32280.07
252H32280.07
261F32330.07
262G32330.07
271F31930.08
272H31930.08
281G32520.07
282H32520.07
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 100 -
Rwork0.326 1968 -
obs--100 %

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