3ebm

Crystal structure of human translationally controlled tumour associated protein (hTCTP) mutant E12V

Method: X-RAY DIFFRACTION

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

Translationally-controlled tumor protein

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TCTP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–172； UniProt 1–172 Author chain B； PDBConstruct 1–172； UniProt 1–172 Author chain C； PDBConstruct 1–172； UniProt 1–172 Author chain D； PDBConstruct 1–172； UniProt 1–172

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	3ebm
Deposition date deposition_date	2008-08-28
Structure title title	Crystal structure of human translationally controlled tumour associated protein (hTCTP) mutant E12V
Keywords keywords	TCTP, E12V, Calcium, Cytoplasm, Phosphoprotein, CALCIUM-BINDING PROTEIN; CALCIUM-BINDING PROTEIN
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.

3ebm__assembly_3__model_1

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

Download this curve (.dat)

3ebm__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ebm__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	16.58 Å
Rg (electron density)	15.22 Å
Total Rg	16.47 Å
Atom count	1192
Residues	145
Excluded volume	21431 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ebm__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ebm__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3ebm__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3ebm__assembly_4__model_1`	monomeric （1）	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)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3ebma1
Class class	b — All beta proteins
Fold Fold fold	b.88 — Mss4-like
Superfamily Superfamily superfamily	b.88.1 — Mss4-like
Family Family family	b.88.1.2 — Translationally controlled tumor protein TCTP (histamine-releasing factor)

Domain ID domain_id	d3ebma2
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	d3ebmb1
Class class	b — All beta proteins
Fold Fold fold	b.88 — Mss4-like
Superfamily Superfamily superfamily	b.88.1 — Mss4-like
Family Family family	b.88.1.2 — Translationally controlled tumor protein TCTP (histamine-releasing factor)

Domain ID domain_id	d3ebmb2
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	d3ebmc1
Class class	b — All beta proteins
Fold Fold fold	b.88 — Mss4-like
Superfamily Superfamily superfamily	b.88.1 — Mss4-like
Family Family family	b.88.1.2 — Translationally controlled tumor protein TCTP (histamine-releasing factor)

Domain ID domain_id	d3ebmc2
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	d3ebmd1
Class class	b — All beta proteins
Fold Fold fold	b.88 — Mss4-like
Superfamily Superfamily superfamily	b.88.1 — Mss4-like
Family Family family	b.88.1.2 — Translationally controlled tumor protein TCTP (histamine-releasing factor)

Domain ID domain_id	d3ebmd2
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	3ebmA00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	10 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A

Domain ID domain_id	3ebmB00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	10 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A

Domain ID domain_id	3ebmC00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	10 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A

Domain ID domain_id	3ebmD00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	10 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A

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Unit-cell length a length_a	78.192 Å
Unit-cell length b length_b	81.543 Å
Unit-cell length c length_c	139.920 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	36.000 Å
R factor r_factor	0.2388
R_work r_work	0.2366
R_free r_free	0.2803

Description description	Translationally-controlled tumor protein
Molecular weight formula_weight	20660.5 kDa
Mutation mutation	E12V
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4825

Crystal structure of human translationally controlled tumour associated protein (hTCTP) mutant E12V

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

Translationally-controlled tumor protein

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

3ebm__assembly_3__model_1

3ebm__assembly_3__model_1 | I(q)

3ebm__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	37

Crystal structure of human translationally controlled tumour associated protein (hTCTP) mutant E12V

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

Translationally-controlled tumor protein

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

3ebm__assembly_3__model_1

3ebm__assembly_3__model_1 | I(q)

3ebm__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)