6c9i

Single-Particle reconstruction of DARP14 - A designed protein scaffold displaying ~17kDa DARPin proteins - Scaffold

Method: ELECTRON MICROSCOPY

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

DARP14 - Subunit A with DARPin

Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	DARP14 - Subunit B × 12 （Q9I2D8）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O58404_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–163； UniProt 1–163 Author chain B； PDBConstruct 1–163； UniProt 1–163 Author chain C； PDBConstruct 1–163； UniProt 1–163 Author chain D； PDBConstruct 1–163； UniProt 1–163 Author chain I； PDBConstruct 1–163； UniProt 1–163 Author chain J； PDBConstruct 1–163； UniProt 1–163 Author chain K； PDBConstruct 1–163； UniProt 1–163 Author chain L； PDBConstruct 1–163； UniProt 1–163 Author chain Q； PDBConstruct 1–163； UniProt 1–163 Author chain R； PDBConstruct 1–163； UniProt 1–163 Author chain S； PDBConstruct 1–163； UniProt 1–163 Author chain T； PDBConstruct 1–163； UniProt 1–163

DARP14 - Subunit B

Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

UniProt Q9I2D8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	DARP14 - Subunit A with DARPin × 12 （O58404）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9I2D8_PSEAE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–123； UniProt 1–123 Author chain F； PDBConstruct 1–123； UniProt 1–123 Author chain G； PDBConstruct 1–123； UniProt 1–123 Author chain H； PDBConstruct 1–123； UniProt 1–123 Author chain M； PDBConstruct 1–123； UniProt 1–123 Author chain N； PDBConstruct 1–123； UniProt 1–123 Author chain O； PDBConstruct 1–123； UniProt 1–123 Author chain P； PDBConstruct 1–123； UniProt 1–123 Author chain U； PDBConstruct 1–123； UniProt 1–123 Author chain V； PDBConstruct 1–123； UniProt 1–123 Author chain W； PDBConstruct 1–123； UniProt 1–123 Author chain X； PDBConstruct 1–123； UniProt 1–123

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	6c9i
Deposition date deposition_date	2018-01-26
Structure title title	Single-Particle reconstruction of DARP14 - A designed protein scaffold displaying ~17kDa DARPin proteins - Scaffold
Keywords keywords	Designed Complex, DARPin, Scaffold, Single-Particle Cryo-EM, DE NOVO PROTEIN; DE NOVO PROTEIN
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.

6c9i__assembly_1__model_1

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

Download this curve (.dat)

6c9i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6c9i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.18 Å
Rg (electron density)	45.15 Å
Total Rg	45.44 Å
Atom count	23700
Residues	3087
Excluded volume	426730 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6c9i__assembly_1__model_1`	24-meric （24）	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 (2)

Entity 1 Entity 1 polymer

Description description	DARP14 - Subunit A with DARPin
Molecular weight formula_weight	18229.3 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,I,J,K,L,Q,R,S,T
Atom count atom_count	23700

MRITTKVGDKGSTRLFGGEEVWKDSPIIEANGTLDELTSFIGEAKHYVDEEMKGILEEIQNDIYKIMGEIGSKGKIEGISEERIAWLLKLILRYMEMVNLKSFVLPGGTLESAKLDVCRTIARRALRKVLTVTREFGIGAEAAAYLLALSDLLFLLARVIEIE

Source Source

Source organism organism	Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
NCBI taxonomy ID ncbi_taxonomy_id	70601
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DARP14 - Subunit B
Molecular weight formula_weight	14346.3 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H,M,N,O,P,U,V,W,X

MPHLVIEATANLRLETSPGELLEQANKALFASGQFGEADIKSRFVTLEAYRQGTAAVERAYLHACLSILDGRDIATRTLLGASLCAVLAEAVAGGGEEGVQVSVEVREMERLSYAKRVVARQRLEHHHHHH

Source Source

Source organism organism	Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
NCBI taxonomy ID ncbi_taxonomy_id	208964
Host organism host_organism	Escherichia coli BL21(DE3)

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6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id	6c9iA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1200 — Hypothetical Protein Ta1238; Chain: A;
Homologous superfamily homologous superfamily	10 — Cobalamin adenosyltransferase-like

Domain ID domain_id	6c9iB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1200 — Hypothetical Protein Ta1238; Chain: A;
Homologous superfamily homologous superfamily	10 — Cobalamin adenosyltransferase-like

Domain ID domain_id	6c9iC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1200 — Hypothetical Protein Ta1238; Chain: A;
Homologous superfamily homologous superfamily	10 — Cobalamin adenosyltransferase-like

Domain ID domain_id	6c9iD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1200 — Hypothetical Protein Ta1238; Chain: A;
Homologous superfamily homologous superfamily	10 — Cobalamin adenosyltransferase-like

Domain ID domain_id	6c9iE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6c9iF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6c9iG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6c9iH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6c9iI00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1200 — Hypothetical Protein Ta1238; Chain: A;
Homologous superfamily homologous superfamily	10 — Cobalamin adenosyltransferase-like

Domain ID domain_id	6c9iJ00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1200 — Hypothetical Protein Ta1238; Chain: A;
Homologous superfamily homologous superfamily	10 — Cobalamin adenosyltransferase-like

Domain ID domain_id	6c9iK00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1200 — Hypothetical Protein Ta1238; Chain: A;
Homologous superfamily homologous superfamily	10 — Cobalamin adenosyltransferase-like

Domain ID domain_id	6c9iL00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1200 — Hypothetical Protein Ta1238; Chain: A;
Homologous superfamily homologous superfamily	10 — Cobalamin adenosyltransferase-like

Domain ID domain_id	6c9iM00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6c9iN00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6c9iO00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6c9iP00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6c9iQ00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1200 — Hypothetical Protein Ta1238; Chain: A;
Homologous superfamily homologous superfamily	10 — Cobalamin adenosyltransferase-like

Domain ID domain_id	6c9iR00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1200 — Hypothetical Protein Ta1238; Chain: A;
Homologous superfamily homologous superfamily	10 — Cobalamin adenosyltransferase-like

Domain ID domain_id	6c9iS00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1200 — Hypothetical Protein Ta1238; Chain: A;
Homologous superfamily homologous superfamily	10 — Cobalamin adenosyltransferase-like

Domain ID domain_id	6c9iT00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1200 — Hypothetical Protein Ta1238; Chain: A;
Homologous superfamily homologous superfamily	10 — Cobalamin adenosyltransferase-like

Domain ID domain_id	6c9iU00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6c9iV00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6c9iW00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	6c9iX00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

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Resolution resolution	3.09 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	34650

Single-Particle reconstruction of DARP14 - A designed protein scaffold displaying ~17kDa DARPin proteins - Scaffold

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

DARP14 - Subunit A with DARPin

State in the Current Structure

Other States of the Same Protein in the Database

DARP14 - Subunit B

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

6c9i__assembly_1__model_1

6c9i__assembly_1__model_1 | I(q)

6c9i__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)

Single-Particle reconstruction of DARP14 - A designed protein scaffold displaying ~17kDa DARPin proteins - Scaffold

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

DARP14 - Subunit A with DARPin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DARP14 - Subunit B

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

6c9i__assembly_1__model_1

6c9i__assembly_1__model_1 | I(q)

6c9i__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)