3vke

Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides

Method: X-RAY DIFFRACTION

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

Poly(rC)-binding protein 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 1	;DNA (5'-D(PAPCPCPCPCPA)-3') ; × 1 water × 2	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 1	;DNA (5'-D(PAPCPCPCPCPA)-3') ; × 1 water × 2	Consistent with all polymers
3	Protein–DNA	Monomer	Protein 1 DNA 1	;DNA (5'-D(PAPCPCPCPCPA)-3') ; × 1 water × 2	Consistent with all polymers
4	Protein–DNA	Monomer	Protein 1 DNA 1	;DNA (5'-D(PAPCPCPCPCPA)-3') ; × 1 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCBP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–75； UniProt 14–86 Author chain B； PDBConstruct 3–75； UniProt 14–86 Author chain C； PDBConstruct 3–75； UniProt 14–86 Author chain D； PDBConstruct 3–75； UniProt 14–86

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	3vke
Deposition date deposition_date	2011-11-15
Structure title title	Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides
Keywords keywords	PCBP-1, DNA RNA BINDING PROTEIN, KH DOMAIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
Experimental Method method	X-RAY DIFFRACTION

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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.

3vke__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3vke__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3vke__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	12.87 Å
Rg (electron density)	11.62 Å
Total Rg	13.01 Å
Atom count	604
Residues	74
Excluded volume	10706 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3vke__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3vke__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3vke__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3vke__assembly_4__model_1`	dimeric （2）	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	Poly(rC)-binding protein 1
Molecular weight formula_weight	8462.8 kDa
Mutation mutation	C54S
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2710

HMLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNSPERIITLTGPTNAIFKAFAMIIDKLEEDINSSW

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PAPCPCPCPCPA)-3') ;
Molecular weight formula_weight	1738.2 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	R,S,T,U

ACCCCA

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	71

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d3vkea1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.51 — Eukaryotic type KH-domain (KH-domain type I)
Superfamily Superfamily superfamily	d.51.1 — Eukaryotic type KH-domain (KH-domain type I)
Family Family family	d.51.1.1 — Eukaryotic type KH-domain (KH-domain type I)

Domain ID domain_id	d3vkea2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3vkea3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3vkeb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.51 — Eukaryotic type KH-domain (KH-domain type I)
Superfamily Superfamily superfamily	d.51.1 — Eukaryotic type KH-domain (KH-domain type I)
Family Family family	d.51.1.1 — Eukaryotic type KH-domain (KH-domain type I)

Domain ID domain_id	d3vkeb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3vkeb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3vkec1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.51 — Eukaryotic type KH-domain (KH-domain type I)
Superfamily Superfamily superfamily	d.51.1 — Eukaryotic type KH-domain (KH-domain type I)
Family Family family	d.51.1.1 — Eukaryotic type KH-domain (KH-domain type I)

Domain ID domain_id	d3vkec2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3vked1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.51 — Eukaryotic type KH-domain (KH-domain type I)
Superfamily Superfamily superfamily	d.51.1 — Eukaryotic type KH-domain (KH-domain type I)
Family Family family	d.51.1.1 — Eukaryotic type KH-domain (KH-domain type I)

Domain ID domain_id	d3vked2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	3vkeA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — K Homology domain, type 1

Domain ID domain_id	3vkeB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — K Homology domain, type 1

Domain ID domain_id	3vkeC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — K Homology domain, type 1

Domain ID domain_id	3vkeD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — K Homology domain, type 1

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Unit-cell length a length_a	38.597 Å
Unit-cell length b length_b	114.887 Å
Unit-cell length c length_c	43.429 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.73 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.770 Å
Low-resolution limit resolution_low	27.160 Å
R factor r_factor	0.1636
R_work r_work	0.1610
R_free r_free	0.2134

Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides

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

Poly(rC)-binding protein 1

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

3vke__assembly_3__model_1

3vke__assembly_3__model_1 | I(q)

3vke__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (10 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides

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

Poly(rC)-binding protein 1

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

3vke__assembly_3__model_1

3vke__assembly_3__model_1 | I(q)

3vke__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (10 domains)

CATH v4.4 (4 domains)

7. Citations (1)