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- PDB-3v3k: Human caspase 9 in complex with bacterial effector protein -

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Basic information

Entry
Database: PDB / ID: 3v3k
TitleHuman caspase 9 in complex with bacterial effector protein
Components
  • Caspase-9
  • Putative uncharacterized protein ECs1815
KeywordsHYDROLASE / Caspase 9
Function / homology
Function and homology information


caspase-9 / caspase complex / peptidase inhibitor activity / Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway ...caspase-9 / caspase complex / peptidase inhibitor activity / Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / Caspase activation via Dependence Receptors in the absence of ligand / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / fibroblast apoptotic process / AKT phosphorylates targets in the cytosol / epithelial cell apoptotic process / platelet formation / Constitutive Signaling by AKT1 E17K in Cancer / protein maturation / enzyme activator activity / signal transduction in response to DNA damage / cellular response to dexamethasone stimulus / intrinsic apoptotic signaling pathway / kidney development / response to ischemia / NOD1/2 Signaling Pathway / protein processing / SH3 domain binding / positive regulation of neuron apoptotic process / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / response to estradiol / peptidase activity / neuron apoptotic process / host cell cytoplasm / response to lipopolysaccharide / response to hypoxia / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / DNA damage response / protein kinase binding / protein-containing complex / mitochondrion / extracellular region / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ferritin - #90 / Effector protein NleF / NleF superfamily / NleF caspase inhibitor / CASP9, CARD domain / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 ...Ferritin - #90 / Effector protein NleF / NleF superfamily / NleF caspase inhibitor / CASP9, CARD domain / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Ferritin / Death-like domain superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Caspase-9 / Effector protein NleF
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.494 Å
AuthorsMoertl, M. / Maskos, K. / Steuber, H.
CitationJournal: Plos One / Year: 2013
Title: Human caspase 9 in complex with bacterial effector protein
Authors: Moertl, M. / Maskos, K. / Steuber, H.
History
DepositionDec 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Feb 28, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-9
B: Putative uncharacterized protein ECs1815
C: Caspase-9
D: Putative uncharacterized protein ECs1815
E: Caspase-9
F: Putative uncharacterized protein ECs1815
G: Caspase-9
H: Putative uncharacterized protein ECs1815
I: Caspase-9
J: Putative uncharacterized protein ECs1815
K: Caspase-9
L: Putative uncharacterized protein ECs1815
M: Caspase-9
N: Putative uncharacterized protein ECs1815
O: Caspase-9
P: Putative uncharacterized protein ECs1815


Theoretical massNumber of molelcules
Total (without water)394,26216
Polymers394,26216
Non-polymers00
Water0
1
A: Caspase-9
B: Putative uncharacterized protein ECs1815


Theoretical massNumber of molelcules
Total (without water)49,2832
Polymers49,2832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Caspase-9
D: Putative uncharacterized protein ECs1815


Theoretical massNumber of molelcules
Total (without water)49,2832
Polymers49,2832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Caspase-9
F: Putative uncharacterized protein ECs1815


Theoretical massNumber of molelcules
Total (without water)49,2832
Polymers49,2832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Caspase-9
H: Putative uncharacterized protein ECs1815


Theoretical massNumber of molelcules
Total (without water)49,2832
Polymers49,2832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Caspase-9
J: Putative uncharacterized protein ECs1815


Theoretical massNumber of molelcules
Total (without water)49,2832
Polymers49,2832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Caspase-9
L: Putative uncharacterized protein ECs1815


Theoretical massNumber of molelcules
Total (without water)49,2832
Polymers49,2832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: Caspase-9
N: Putative uncharacterized protein ECs1815


Theoretical massNumber of molelcules
Total (without water)49,2832
Polymers49,2832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
O: Caspase-9
P: Putative uncharacterized protein ECs1815


Theoretical massNumber of molelcules
Total (without water)49,2832
Polymers49,2832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.703, 209.906, 317.231
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
21E
31I
41M
12C
22G
32K
42O
13B
23F
33J
43N
14D
24H
34L
44P

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A151 - 156
2115E151 - 156
3115I151 - 156
4115M151 - 156
1215A162 - 174
2215E162 - 174
3215I162 - 174
4215M162 - 174
1315A176 - 189
2315E176 - 189
3315I176 - 189
4315M176 - 189
1415A192 - 208
2415E192 - 208
3415I192 - 208
4415M192 - 208
1515A211 - 216
2515E211 - 216
3515I211 - 216
4515M211 - 216
1615A217 - 219
2615E217 - 219
3615I217 - 219
4615M217 - 219
1715A220 - 239
2715E220 - 239
3715I220 - 239
4715M220 - 239
1815A242 - 258
2815E242 - 258
3815I242 - 258
4815M242 - 258
1915A260 - 294
2915E260 - 294
3915I260 - 294
4915M260 - 294
11015A321 - 343
21015E321 - 343
31015I321 - 343
41015M321 - 343
11115A347 - 395
21115E347 - 395
31115I347 - 395
41115M347 - 395
1125C151 - 156
2125G151 - 156
3125K151 - 156
4125O151 - 156
1225C162 - 174
2225G162 - 174
3225K162 - 174
4225O162 - 174
1325C176 - 189
2325G176 - 189
3325K176 - 189
4325O176 - 189
1425C192 - 208
2425G192 - 208
3425K192 - 208
4425O192 - 208
1525C211 - 216
2525G211 - 216
3525K211 - 216
4525O211 - 216
1625C217 - 219
2625G217 - 219
3625K217 - 219
4625O217 - 219
1725C220 - 239
2725G220 - 239
3725K220 - 239
4725O220 - 239
1825C242 - 258
2825G242 - 258
3825K242 - 258
4825O242 - 258
1925C260 - 294
2925G260 - 294
3925K260 - 294
4925O260 - 294
11025C321 - 343
21025G321 - 343
31025K321 - 343
41025O321 - 343
11125C347 - 395
21125G347 - 395
31125K347 - 395
41125O347 - 395
1135B1 - 30
2135F1 - 30
3135J1 - 30
4135N1 - 30
1235B32 - 40
2235F32 - 40
3235J32 - 40
4235N32 - 40
1335B42 - 56
2335F42 - 56
3335J42 - 56
4335N42 - 56
1435B58 - 98
2435F58 - 98
3435J58 - 98
4435N58 - 98
1535B99 - 127
2535F99 - 127
3535J99 - 127
4535N99 - 127
1635B135 - 164
2635F135 - 164
3635J135 - 164
4635N135 - 164
1735B173 - 184
2735F173 - 184
3735J173 - 184
4735N173 - 184
1145D1 - 30
2145H1 - 30
3145L1 - 30
4145P1 - 30
1245D32 - 40
2245H32 - 40
3245L32 - 40
4245P32 - 40
1345D42 - 56
2345H42 - 56
3345L42 - 56
4345P42 - 56
1445D58 - 98
2445H58 - 98
3445L58 - 98
4445P58 - 98
1545D99 - 127
2545H99 - 127
3545L99 - 127
4545P99 - 127
1645D135 - 164
2645H135 - 164
3645L135 - 164
4645P135 - 164
1745D173 - 184
2745H173 - 184
3745L173 - 184
4745P173 - 184

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
Caspase-9 / / CASP-9 / Apoptotic protease Mch-6 / Apoptotic protease-activating factor 3 / APAF-3 / ICE-like ...CASP-9 / Apoptotic protease Mch-6 / Apoptotic protease-activating factor 3 / APAF-3 / ICE-like apoptotic protease 6 / ICE-LAP6 / Caspase-9 subunit p35 / Caspase-9 subunit p10


Mass: 30416.570 Da / Num. of mol.: 8 / Fragment: UNP Residues 141-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP9, MCH6 / Production host: Escherichia coli (E. coli) / References: UniProt: P55211, caspase-9
#2: Protein
Putative uncharacterized protein ECs1815


Mass: 18866.186 Da / Num. of mol.: 8 / Fragment: UNP Residues 25-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: ECs1815, Z6020 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XAL7
Sequence detailsTHE Q221R MUTATION IS A NATURAL VARIANT OF THE PROTEIN

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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: 4.16 Å3/Da / Density % sol: 70.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.75 K-Na-Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0015 / Wavelength: 1.0015 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2010
RadiationMonochromator: Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0015 Å / Relative weight: 1
ReflectionResolution: 3.49→174.08 Å / Num. all: 86121 / Num. obs: 86121 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 5.9
Reflection shellResolution: 3.49→3.77 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.3 / % possible all: 98.3

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 3.494→174.08 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.883 / SU B: 28.541 / SU ML: 0.426 / Cross valid method: THROUGHOUT / ESU R Free: 0.498 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25949 1689 2 %RANDOM
Rwork0.23923 ---
all0.248 84730 --
obs0.23963 83041 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 67.695 Å2
Baniso -1Baniso -2Baniso -3
1-3.83 Å20 Å20 Å2
2---2.09 Å20 Å2
3----1.75 Å2
Refinement stepCycle: LAST / Resolution: 3.494→174.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25428 0 0 0 25428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02124986
X-RAY DIFFRACTIONr_bond_other_d0.0010.0217195
X-RAY DIFFRACTIONr_angle_refined_deg0.9321.95533831
X-RAY DIFFRACTIONr_angle_other_deg0.931341374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.19553213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99723.7971056
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.477154017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.03215137
X-RAY DIFFRACTIONr_chiral_restr0.0520.23822
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02128201
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025180
X-RAY DIFFRACTIONr_mcbond_it0.745216073
X-RAY DIFFRACTIONr_mcbond_other0.05926563
X-RAY DIFFRACTIONr_mcangle_it1.402325685
X-RAY DIFFRACTIONr_scbond_it1.02948913
X-RAY DIFFRACTIONr_scangle_it1.84868146
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1163MEDIUM POSITIONAL0.080.5
12E1163MEDIUM POSITIONAL0.10.5
13I1163MEDIUM POSITIONAL0.090.5
14M1163MEDIUM POSITIONAL0.080.5
11A1388LOOSE POSITIONAL0.35
12E1388LOOSE POSITIONAL0.315
13I1388LOOSE POSITIONAL0.35
14M1388LOOSE POSITIONAL0.235
11A1163MEDIUM THERMAL0.092
12E1163MEDIUM THERMAL0.082
13I1163MEDIUM THERMAL0.092
14M1163MEDIUM THERMAL0.082
11A1388LOOSE THERMAL0.0910
12E1388LOOSE THERMAL0.0810
13I1388LOOSE THERMAL0.0910
14M1388LOOSE THERMAL0.0710
21C1163MEDIUM POSITIONAL0.090.5
22G1163MEDIUM POSITIONAL0.10.5
23K1163MEDIUM POSITIONAL0.090.5
24O1163MEDIUM POSITIONAL0.10.5
21C1395LOOSE POSITIONAL0.35
22G1395LOOSE POSITIONAL0.365
23K1395LOOSE POSITIONAL0.35
24O1395LOOSE POSITIONAL0.255
21C1163MEDIUM THERMAL0.092
22G1163MEDIUM THERMAL0.082
23K1163MEDIUM THERMAL0.082
24O1163MEDIUM THERMAL0.092
21C1395LOOSE THERMAL0.0910
22G1395LOOSE THERMAL0.0710
23K1395LOOSE THERMAL0.0710
24O1395LOOSE THERMAL0.0910
31B841MEDIUM POSITIONAL0.080.5
32F841MEDIUM POSITIONAL0.090.5
33J841MEDIUM POSITIONAL0.10.5
34N841MEDIUM POSITIONAL0.080.5
31B965LOOSE POSITIONAL0.115
32F965LOOSE POSITIONAL0.145
33J965LOOSE POSITIONAL0.145
34N965LOOSE POSITIONAL0.125
31B841MEDIUM THERMAL0.062
32F841MEDIUM THERMAL0.072
33J841MEDIUM THERMAL0.062
34N841MEDIUM THERMAL0.082
31B965LOOSE THERMAL0.0710
32F965LOOSE THERMAL0.0710
33J965LOOSE THERMAL0.0610
34N965LOOSE THERMAL0.0910
41D836MEDIUM POSITIONAL0.080.5
42H836MEDIUM POSITIONAL0.10.5
43L836MEDIUM POSITIONAL0.080.5
44P836MEDIUM POSITIONAL0.080.5
41D905LOOSE POSITIONAL0.125
42H905LOOSE POSITIONAL0.145
43L905LOOSE POSITIONAL0.135
44P905LOOSE POSITIONAL0.135
41D836MEDIUM THERMAL0.062
42H836MEDIUM THERMAL0.12
43L836MEDIUM THERMAL0.082
44P836MEDIUM THERMAL0.072
41D905LOOSE THERMAL0.0610
42H905LOOSE THERMAL0.110
43L905LOOSE THERMAL0.0710
44P905LOOSE THERMAL0.0710
LS refinement shellResolution: 3.494→3.585 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 148 -
Rwork0.323 5933 -
obs--96.62 %

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