SAXSdb — 8yw6

▼

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

Mitochondrial pyruvate carrier 2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	MPC specific nanobody 1 × 1 Mitochondrial pyruvate carrier 1 × 1 （Q9Y5U8） 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 CARDIOLIPIN × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MPC2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–127； UniProt 1–127

Mitochondrial pyruvate carrier 1

Homo sapiens

UniProt Q9Y5U8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Mitochondrial pyruvate carrier 2 × 1 （O95563） MPC specific nanobody 1 × 1 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 CARDIOLIPIN × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MPC1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–109； UniProt 1–109

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8yw6
Deposition date deposition_date	2024-03-29
Structure title title	Cryo-EM structure of apo human mitochondrial pyruvate carrier in the IMS-open conformation at pH 8.0
Keywords keywords	mitochondrial pyruvate carrier, MPC, pyruvate transport, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

8yw6__assembly_1__model_1

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

Download this curve (.dat)

8yw6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8yw6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.84 Å
Rg (electron density)	27.17 Å
Total Rg	27.77 Å
Atom count	2747
Residues	333
Excluded volume	49680 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8yw6__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Mitochondrial pyruvate carrier 2
Molecular weight formula_weight	17161.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	2747

MSAAGARGLRATYHRLLDKVELMLPEKLRPLYNHPAGPRTVFFWAPIMKWGLVCAGLADMARPAEKLSTAQSAVLMATGFIWSRYSLVIIPKNWSLFAVNFFVGAAGASQLFRIWRYNQELKAKAHKGSDYKDHDGDYKDHDIDYKDDDDK

Source Source

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

Entity 2 Entity 2 polymer

Description description	MPC specific nanobody 1
Molecular weight formula_weight	15255.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

EVQLVESGGGLVQAGGSLRLSCAASGFPVTERVMYWYRQAPGKEREWVAAIDSQGSSTYYADSVKGRFTISRDNSKNTVYLQMNSLKPEDTAVYYCKVEVGWGYKGQGTQVTVSSLEHHHHHHHGGSGEQKLISEEDL

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Mitochondrial pyruvate carrier 1
Molecular weight formula_weight	13592.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MAGALVRKAADYVRSKDFRDYLMSTHFWGPVANWGLPIAAINDMKKSPEIISGRMTFALCCYSLTFMRFAYKVQPRNWLLFACHATNEVAQLIQGGRLIKHEMTKTASAGSYPYDVPDYA

Source Source

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

Entity 4 Entity 4 non-polymer

Description description	1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Molecular weight formula_weight	510.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CARDIOLIPIN
Molecular weight formula_weight	1464.0 kDa
Source method src_method	syn
Copy count entity_count	1

▶

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	—

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

Resolution resolution	3.18 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	474010

Cryo-EM structure of apo human mitochondrial pyruvate carrier in the IMS-open conformation at pH 8.0

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

Mitochondrial pyruvate carrier 2

State in the Current Structure

Other States of the Same Protein in the Database

Mitochondrial pyruvate carrier 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

8yw6__assembly_1__model_1

8yw6__assembly_1__model_1 | I(q)

8yw6__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)

Cryo-EM structure of apo human mitochondrial pyruvate carrier in the IMS-open conformation at pH 8.0

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

Mitochondrial pyruvate carrier 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Mitochondrial pyruvate carrier 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

8yw6__assembly_1__model_1

8yw6__assembly_1__model_1 | I(q)

8yw6__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)