SAXSdb — 3j9k

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Apaf-1 related killer DARK

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 32	Caspase Nc × 16 （Q9XYF4） ADENOSINE-5'-DIPHOSPHATE × 16	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7KLI1_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–583； UniProt 1–583 Author chain C； PDBConstruct 1–583； UniProt 1–583 Author chain E； PDBConstruct 1–583； UniProt 1–583 Author chain G； PDBConstruct 1–583； UniProt 1–583 Author chain I； PDBConstruct 1–583； UniProt 1–583 Author chain K； PDBConstruct 1–583； UniProt 1–583 Author chain M； PDBConstruct 1–583； UniProt 1–583 Author chain O； PDBConstruct 1–583； UniProt 1–583 Author chain Q； PDBConstruct 1–583； UniProt 1–583 Author chain S； PDBConstruct 1–583； UniProt 1–583 Author chain U； PDBConstruct 1–583； UniProt 1–583 Author chain W； PDBConstruct 1–583； UniProt 1–583 Author chain Y； PDBConstruct 1–583； UniProt 1–583 Author chain a； PDBConstruct 1–583； UniProt 1–583 Author chain c； PDBConstruct 1–583； UniProt 1–583 Author chain e； PDBConstruct 1–583； UniProt 1–583

Caspase Nc

OrganismNot specified

UniProt Q9XYF4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 32	Apaf-1 related killer DARK × 16 （Q7KLI1） ADENOSINE-5'-DIPHOSPHATE × 16	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ICENC_DROME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–450； UniProt 1–450 Author chain D； PDBConstruct 1–450； UniProt 1–450 Author chain F； PDBConstruct 1–450； UniProt 1–450 Author chain H； PDBConstruct 1–450； UniProt 1–450 Author chain J； PDBConstruct 1–450； UniProt 1–450 Author chain L； PDBConstruct 1–450； UniProt 1–450 Author chain N； PDBConstruct 1–450； UniProt 1–450 Author chain P； PDBConstruct 1–450； UniProt 1–450 Author chain R； PDBConstruct 1–450； UniProt 1–450 Author chain T； PDBConstruct 1–450； UniProt 1–450 Author chain V； PDBConstruct 1–450； UniProt 1–450 Author chain X； PDBConstruct 1–450； UniProt 1–450 Author chain Z； PDBConstruct 1–450； UniProt 1–450 Author chain b； PDBConstruct 1–450； UniProt 1–450 Author chain d； PDBConstruct 1–450； UniProt 1–450 Author chain f； PDBConstruct 1–450； UniProt 1–450

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3j9k
Deposition date deposition_date	2015-02-04
Structure title title	Structure of Dark apoptosome in complex with Dronc CARD domain
Keywords keywords	programmed cell death, caspase activation, APOPTOSIS; APOPTOSIS
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3j9k__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3j9k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3j9k__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	99.01 Å
Rg (electron density)	96.20 Å
Total Rg	95.21 Å
Atom count	126512
Residues	18640
Excluded volume	2199900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3j9k__assembly_1__model_1`	32-meric （32）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Apaf-1 related killer DARK
Molecular weight formula_weight	112749.2 kDa
Source method src_method	nat
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K,M,O,Q,S,U,W,Y,a,c,e
Atom count atom_count	126512

MDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQVQRXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 2 Entity 2 polymer

Description description	Caspase Nc
Molecular weight formula_weight	51207.1 kDa
EC 编号 ec_number	3.4.22.-
Source method src_method	nat
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L,N,P,R,T,V,X,Z,b,d,f

MQPPELEIGMPKRHREHIRKNLNILVEWTNYERLAMECVQQGILTVQMLRNTQDLNGKPFNMDEKDVRVEQHRRLLLKITQRGPTAYNLLINALRNINCLDAAVLLESVDESDSRPPFISLNERRTSRKSADIVDTPSPEASEGPCVSKLRNEPLGALTPYVGVVDGPEVKKSKKIHGGDSAILGTYKMQSRFNRGVLLMVNIMDYPDQNRRRIGAEKDSKSLIHLFQELNFTIFPYGNVNQDQFFKLLTMVTSSSYVQNTECFVMVLMTHGNSVEGKEKVEFCDGSVVDMQKIKDHFQTAKCPYLVNKPKVLMFPFCRGDEYDLGHPKNQGNLMEPVYTAQEEKWPDTQTEGIPSPSTNVPSLADTLVCYANTPGYVTHRDLDTGSWYIQKFCQVMADHAHDTDLEDILKKTSEAVGNKRTKKGSMQTGAYDNLGFNKKLYFNPGFFNE

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	16

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	4.10 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	11359

Structure of Dark apoptosome in complex with Dronc CARD domain

1. Protein Identity and Related Structures Protein Identity & Related Structures

Apaf-1 related killer DARK

State in the Current Structure

Other States of the Same Protein in the Database

Caspase Nc

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3j9k__assembly_1__model_1

3j9k__assembly_1__model_1 | I(q)

3j9k__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

7. Citations (1)

Structure of Dark apoptosome in complex with Dronc CARD domain

1. Protein Identity and Related Structures Protein Identity & Related Structures

Apaf-1 related killer DARK

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Caspase Nc

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3j9k__assembly_1__model_1

3j9k__assembly_1__model_1 | I(q)

3j9k__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

7. Citations (1)