9ya3

Cryo-EM structure of the apical region of subpellicular microtubule (SPMT) from Toxoplasma gondii (8-nm repeat)

Method: ELECTRON MICROSCOPY Dmax: 338.1 Å Quality: GOOD

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

Microtubule associated protein SPM1

OrganismNot specified

UniProt A0A7J6K285

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 108 PDB declaration: 108-meric(108) Consistent with protein copy count Chain 0; UniProt 1–351 Chain 1; UniProt 1–351 Chain 10; UniProt 1–351 Chain 11; UniProt 1–351 Chain 12; UniProt 1–351 Chain 13; UniProt 1–351 Chain 14; UniProt 1–351 Chain 15; UniProt 1–351 Chain 16; UniProt 1–351 Chain 17; UniProt 1–351 Chain 18; UniProt 1–351 Chain 19; UniProt 1–351 Chain 2; UniProt 1–351 Chain 22; UniProt 1–351 Chain 23; UniProt 1–351 Chain 3; UniProt 1–351 Chain 4; UniProt 1–351 Chain 5; UniProt 1–351 Chain 6; UniProt 1–351 Chain 7; UniProt 1–351 Chain 8; UniProt 1–351 Chain 9; UniProt 1–351 Not recorded TLAP3 (apical cap protein AC5), TGME49_235380 × 3 (A0A151H4L4) Tubulin alpha chain × 26 (P10873) Tubulin beta chain × 26 (I7BFC9) TLAP4 (thioredoxin-like associated protein), TGME49_201760 × 3 (A0A7J6K913) TLAP2 (thioredoxin-like associated protein), TGME49_232130 × 4 (A0A125YLA3) TRXL1, TGME49_232410 × 22 (Q8MPF4) TRXL2, TGME49_225790 × 2 (A0A7J6K232) GDP GUANOSINE-5'-DIPHOSPHATE × 26 GTP GUANOSINE-5'-TRIPHOSPHATE × 26 MG MAGNESIUM ION × 26 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A7J6K285_TOXGO
Isoform
PDB entities 1
Chains and sequence ranges Author chain 0; PDBConstruct 1–351; UniProt 1–351 Author chain 1; PDBConstruct 1–351; UniProt 1–351 Author chain 10; PDBConstruct 1–351; UniProt 1–351 Author chain 11; PDBConstruct 1–351; UniProt 1–351 Author chain 12; PDBConstruct 1–351; UniProt 1–351 Author chain 13; PDBConstruct 1–351; UniProt 1–351 Author chain 14; PDBConstruct 1–351; UniProt 1–351 Author chain 15; PDBConstruct 1–351; UniProt 1–351 Author chain 16; PDBConstruct 1–351; UniProt 1–351 Author chain 17; PDBConstruct 1–351; UniProt 1–351 Author chain 18; PDBConstruct 1–351; UniProt 1–351 Author chain 19; PDBConstruct 1–351; UniProt 1–351 Author chain 2; PDBConstruct 1–351; UniProt 1–351 Author chain 22; PDBConstruct 1–351; UniProt 1–351 Author chain 23; PDBConstruct 1–351; UniProt 1–351 Author chain 3; PDBConstruct 1–351; UniProt 1–351 Author chain 4; PDBConstruct 1–351; UniProt 1–351 Author chain 5; PDBConstruct 1–351; UniProt 1–351 Author chain 6; PDBConstruct 1–351; UniProt 1–351 Author chain 7; PDBConstruct 1–351; UniProt 1–351 Author chain 8; PDBConstruct 1–351; UniProt 1–351 Author chain 9; PDBConstruct 1–351; UniProt 1–351

TLAP3 (apical cap protein AC5), TGME49_235380

OrganismNot specified

UniProt A0A151H4L4

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 108 PDB declaration: 108-meric(108) Consistent with protein copy count Chain A; UniProt 1–583 Chain B; UniProt 1–583 Chain C; UniProt 1–583 Not recorded Microtubule associated protein SPM1 × 22 (A0A7J6K285) Tubulin alpha chain × 26 (P10873) Tubulin beta chain × 26 (I7BFC9) TLAP4 (thioredoxin-like associated protein), TGME49_201760 × 3 (A0A7J6K913) TLAP2 (thioredoxin-like associated protein), TGME49_232130 × 4 (A0A125YLA3) TRXL1, TGME49_232410 × 22 (Q8MPF4) TRXL2, TGME49_225790 × 2 (A0A7J6K232) GDP GUANOSINE-5'-DIPHOSPHATE × 26 GTP GUANOSINE-5'-TRIPHOSPHATE × 26 MG MAGNESIUM ION × 26 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A151H4L4_TOXGO
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 1–583; UniProt 1–583 Author chain B; PDBConstruct 1–583; UniProt 1–583 Author chain C; PDBConstruct 1–583; UniProt 1–583

Tubulin alpha chain

OrganismNot specified

UniProt P10873

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 108 PDB declaration: 108-meric(108) Consistent with protein copy count Chain A0; UniProt 1–453 Chain A2; UniProt 1–453 Chain A4; UniProt 1–453 Chain A6; UniProt 1–453 Chain A8; UniProt 1–453 Chain B0; UniProt 1–453 Chain B2; UniProt 1–453 Chain B4; UniProt 1–453 Chain B6; UniProt 1–453 Chain B8; UniProt 1–453 Chain C0; UniProt 1–453 Chain C2; UniProt 1–453 Chain C4; UniProt 1–453 Chain C6; UniProt 1–453 Chain C8; UniProt 1–453 Chain D0; UniProt 1–453 Chain D2; UniProt 1–453 Chain D4; UniProt 1–453 Chain D6; UniProt 1–453 Chain D8; UniProt 1–453 Chain E0; UniProt 1–453 Chain E2; UniProt 1–453 Chain E4; UniProt 1–453 Chain E6; UniProt 1–453 Chain E8; UniProt 1–453 Chain F0; UniProt 1–453 Not recorded Microtubule associated protein SPM1 × 22 (A0A7J6K285) TLAP3 (apical cap protein AC5), TGME49_235380 × 3 (A0A151H4L4) Tubulin beta chain × 26 (I7BFC9) TLAP4 (thioredoxin-like associated protein), TGME49_201760 × 3 (A0A7J6K913) TLAP2 (thioredoxin-like associated protein), TGME49_232130 × 4 (A0A125YLA3) TRXL1, TGME49_232410 × 22 (Q8MPF4) TRXL2, TGME49_225790 × 2 (A0A7J6K232) GDP GUANOSINE-5'-DIPHOSPHATE × 26 GTP GUANOSINE-5'-TRIPHOSPHATE × 26 MG MAGNESIUM ION × 26 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBA_TOXGO
Isoform
PDB entities 3
Chains and sequence ranges Author chain A0; PDBConstruct 1–453; UniProt 1–453 Author chain A2; PDBConstruct 1–453; UniProt 1–453 Author chain A4; PDBConstruct 1–453; UniProt 1–453 Author chain A6; PDBConstruct 1–453; UniProt 1–453 Author chain A8; PDBConstruct 1–453; UniProt 1–453 Author chain B0; PDBConstruct 1–453; UniProt 1–453 Author chain B2; PDBConstruct 1–453; UniProt 1–453 Author chain B4; PDBConstruct 1–453; UniProt 1–453 Author chain B6; PDBConstruct 1–453; UniProt 1–453 Author chain B8; PDBConstruct 1–453; UniProt 1–453 Author chain C0; PDBConstruct 1–453; UniProt 1–453 Author chain C2; PDBConstruct 1–453; UniProt 1–453 Author chain C4; PDBConstruct 1–453; UniProt 1–453 Author chain C6; PDBConstruct 1–453; UniProt 1–453 Author chain C8; PDBConstruct 1–453; UniProt 1–453 Author chain D0; PDBConstruct 1–453; UniProt 1–453 Author chain D2; PDBConstruct 1–453; UniProt 1–453 Author chain D4; PDBConstruct 1–453; UniProt 1–453 Author chain D6; PDBConstruct 1–453; UniProt 1–453 Author chain D8; PDBConstruct 1–453; UniProt 1–453 Author chain E0; PDBConstruct 1–453; UniProt 1–453 Author chain E2; PDBConstruct 1–453; UniProt 1–453 Author chain E4; PDBConstruct 1–453; UniProt 1–453 Author chain E6; PDBConstruct 1–453; UniProt 1–453 Author chain E8; PDBConstruct 1–453; UniProt 1–453 Author chain F0; PDBConstruct 1–453; UniProt 1–453

Tubulin beta chain

OrganismNot specified

UniProt I7BFC9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 108 PDB declaration: 108-meric(108) Consistent with protein copy count Chain A1; UniProt 1–449 Chain A3; UniProt 1–449 Chain A5; UniProt 1–449 Chain A7; UniProt 1–449 Chain A9; UniProt 1–449 Chain B1; UniProt 1–449 Chain B3; UniProt 1–449 Chain B5; UniProt 1–449 Chain B7; UniProt 1–449 Chain B9; UniProt 1–449 Chain C1; UniProt 1–449 Chain C3; UniProt 1–449 Chain C5; UniProt 1–449 Chain C7; UniProt 1–449 Chain C9; UniProt 1–449 Chain D1; UniProt 1–449 Chain D3; UniProt 1–449 Chain D5; UniProt 1–449 Chain D7; UniProt 1–449 Chain D9; UniProt 1–449 Chain E1; UniProt 1–449 Chain E3; UniProt 1–449 Chain E5; UniProt 1–449 Chain E7; UniProt 1–449 Chain E9; UniProt 1–449 Chain F1; UniProt 1–449 Not recorded Microtubule associated protein SPM1 × 22 (A0A7J6K285) TLAP3 (apical cap protein AC5), TGME49_235380 × 3 (A0A151H4L4) Tubulin alpha chain × 26 (P10873) TLAP4 (thioredoxin-like associated protein), TGME49_201760 × 3 (A0A7J6K913) TLAP2 (thioredoxin-like associated protein), TGME49_232130 × 4 (A0A125YLA3) TRXL1, TGME49_232410 × 22 (Q8MPF4) TRXL2, TGME49_225790 × 2 (A0A7J6K232) GDP GUANOSINE-5'-DIPHOSPHATE × 26 GTP GUANOSINE-5'-TRIPHOSPHATE × 26 MG MAGNESIUM ION × 26 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name I7BFC9_TOXGO
Isoform
PDB entities 4
Chains and sequence ranges Author chain A1; PDBConstruct 1–449; UniProt 1–449 Author chain A3; PDBConstruct 1–449; UniProt 1–449 Author chain A5; PDBConstruct 1–449; UniProt 1–449 Author chain A7; PDBConstruct 1–449; UniProt 1–449 Author chain A9; PDBConstruct 1–449; UniProt 1–449 Author chain B1; PDBConstruct 1–449; UniProt 1–449 Author chain B3; PDBConstruct 1–449; UniProt 1–449 Author chain B5; PDBConstruct 1–449; UniProt 1–449 Author chain B7; PDBConstruct 1–449; UniProt 1–449 Author chain B9; PDBConstruct 1–449; UniProt 1–449 Author chain C1; PDBConstruct 1–449; UniProt 1–449 Author chain C3; PDBConstruct 1–449; UniProt 1–449 Author chain C5; PDBConstruct 1–449; UniProt 1–449 Author chain C7; PDBConstruct 1–449; UniProt 1–449 Author chain C9; PDBConstruct 1–449; UniProt 1–449 Author chain D1; PDBConstruct 1–449; UniProt 1–449 Author chain D3; PDBConstruct 1–449; UniProt 1–449 Author chain D5; PDBConstruct 1–449; UniProt 1–449 Author chain D7; PDBConstruct 1–449; UniProt 1–449 Author chain D9; PDBConstruct 1–449; UniProt 1–449 Author chain E1; PDBConstruct 1–449; UniProt 1–449 Author chain E3; PDBConstruct 1–449; UniProt 1–449 Author chain E5; PDBConstruct 1–449; UniProt 1–449 Author chain E7; PDBConstruct 1–449; UniProt 1–449 Author chain E9; PDBConstruct 1–449; UniProt 1–449 Author chain F1; PDBConstruct 1–449; UniProt 1–449

TLAP4 (thioredoxin-like associated protein), TGME49_201760

OrganismNot specified

UniProt A0A7J6K913

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 108 PDB declaration: 108-meric(108) Consistent with protein copy count Chain E; UniProt 1–336 Chain F; UniProt 1–336 Chain G; UniProt 1–336 Not recorded Microtubule associated protein SPM1 × 22 (A0A7J6K285) TLAP3 (apical cap protein AC5), TGME49_235380 × 3 (A0A151H4L4) Tubulin alpha chain × 26 (P10873) Tubulin beta chain × 26 (I7BFC9) TLAP2 (thioredoxin-like associated protein), TGME49_232130 × 4 (A0A125YLA3) TRXL1, TGME49_232410 × 22 (Q8MPF4) TRXL2, TGME49_225790 × 2 (A0A7J6K232) GDP GUANOSINE-5'-DIPHOSPHATE × 26 GTP GUANOSINE-5'-TRIPHOSPHATE × 26 MG MAGNESIUM ION × 26 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A7J6K913_TOXGO
Isoform
PDB entities 5
Chains and sequence ranges Author chain E; PDBConstruct 1–336; UniProt 1–336 Author chain F; PDBConstruct 1–336; UniProt 1–336 Author chain G; PDBConstruct 1–336; UniProt 1–336

TLAP2 (thioredoxin-like associated protein), TGME49_232130

OrganismNot specified

UniProt A0A125YLA3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 108 PDB declaration: 108-meric(108) Consistent with protein copy count Chain H; UniProt 1–446 Chain I; UniProt 1–446 Chain J; UniProt 1–446 Chain K; UniProt 1–446 Not recorded Microtubule associated protein SPM1 × 22 (A0A7J6K285) TLAP3 (apical cap protein AC5), TGME49_235380 × 3 (A0A151H4L4) Tubulin alpha chain × 26 (P10873) Tubulin beta chain × 26 (I7BFC9) TLAP4 (thioredoxin-like associated protein), TGME49_201760 × 3 (A0A7J6K913) TRXL1, TGME49_232410 × 22 (Q8MPF4) TRXL2, TGME49_225790 × 2 (A0A7J6K232) GDP GUANOSINE-5'-DIPHOSPHATE × 26 GTP GUANOSINE-5'-TRIPHOSPHATE × 26 MG MAGNESIUM ION × 26 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A125YLA3_TOXGM
Isoform
PDB entities 6
Chains and sequence ranges Author chain H; PDBConstruct 1–446; UniProt 1–446 Author chain I; PDBConstruct 1–446; UniProt 1–446 Author chain J; PDBConstruct 1–446; UniProt 1–446 Author chain K; PDBConstruct 1–446; UniProt 1–446

TRXL1, TGME49_232410

OrganismNot specified

UniProt Q8MPF4

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 108 PDB declaration: 108-meric(108) Consistent with protein copy count Chain a; UniProt 1–220 Chain b; UniProt 1–220 Chain c; UniProt 1–220 Chain d; UniProt 1–220 Chain e; UniProt 1–220 Chain f; UniProt 1–220 Chain g; UniProt 1–220 Chain h; UniProt 1–220 Chain i; UniProt 1–220 Chain j; UniProt 1–220 Chain m; UniProt 1–220 Chain n; UniProt 1–220 Chain o; UniProt 1–220 Chain p; UniProt 1–220 Chain q; UniProt 1–220 Chain r; UniProt 1–220 Chain s; UniProt 1–220 Chain t; UniProt 1–220 Chain u; UniProt 1–220 Chain v; UniProt 1–220 Chain w; UniProt 1–220 Chain x; UniProt 1–220 Not recorded Microtubule associated protein SPM1 × 22 (A0A7J6K285) TLAP3 (apical cap protein AC5), TGME49_235380 × 3 (A0A151H4L4) Tubulin alpha chain × 26 (P10873) Tubulin beta chain × 26 (I7BFC9) TLAP4 (thioredoxin-like associated protein), TGME49_201760 × 3 (A0A7J6K913) TLAP2 (thioredoxin-like associated protein), TGME49_232130 × 4 (A0A125YLA3) TRXL2, TGME49_225790 × 2 (A0A7J6K232) GDP GUANOSINE-5'-DIPHOSPHATE × 26 GTP GUANOSINE-5'-TRIPHOSPHATE × 26 MG MAGNESIUM ION × 26 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q8MPF4_TOXGO
Isoform
PDB entities 7
Chains and sequence ranges Author chain a; PDBConstruct 1–220; UniProt 1–220 Author chain b; PDBConstruct 1–220; UniProt 1–220 Author chain c; PDBConstruct 1–220; UniProt 1–220 Author chain d; PDBConstruct 1–220; UniProt 1–220 Author chain e; PDBConstruct 1–220; UniProt 1–220 Author chain f; PDBConstruct 1–220; UniProt 1–220 Author chain g; PDBConstruct 1–220; UniProt 1–220 Author chain h; PDBConstruct 1–220; UniProt 1–220 Author chain i; PDBConstruct 1–220; UniProt 1–220 Author chain j; PDBConstruct 1–220; UniProt 1–220 Author chain m; PDBConstruct 1–220; UniProt 1–220 Author chain n; PDBConstruct 1–220; UniProt 1–220 Author chain o; PDBConstruct 1–220; UniProt 1–220 Author chain p; PDBConstruct 1–220; UniProt 1–220 Author chain q; PDBConstruct 1–220; UniProt 1–220 Author chain r; PDBConstruct 1–220; UniProt 1–220 Author chain s; PDBConstruct 1–220; UniProt 1–220 Author chain t; PDBConstruct 1–220; UniProt 1–220 Author chain u; PDBConstruct 1–220; UniProt 1–220 Author chain v; PDBConstruct 1–220; UniProt 1–220 Author chain w; PDBConstruct 1–220; UniProt 1–220 Author chain x; PDBConstruct 1–220; UniProt 1–220

TRXL2, TGME49_225790

OrganismNot specified

UniProt A0A7J6K232

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 108 PDB declaration: 108-meric(108) Consistent with protein copy count Chain k; UniProt 1–166 Chain l; UniProt 1–166 Not recorded Microtubule associated protein SPM1 × 22 (A0A7J6K285) TLAP3 (apical cap protein AC5), TGME49_235380 × 3 (A0A151H4L4) Tubulin alpha chain × 26 (P10873) Tubulin beta chain × 26 (I7BFC9) TLAP4 (thioredoxin-like associated protein), TGME49_201760 × 3 (A0A7J6K913) TLAP2 (thioredoxin-like associated protein), TGME49_232130 × 4 (A0A125YLA3) TRXL1, TGME49_232410 × 22 (Q8MPF4) GDP GUANOSINE-5'-DIPHOSPHATE × 26 GTP GUANOSINE-5'-TRIPHOSPHATE × 26 MG MAGNESIUM ION × 26 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A7J6K232_TOXGO
Isoform
PDB entities 8
Chains and sequence ranges Author chain k; PDBConstruct 1–166; UniProt 1–166 Author chain l; PDBConstruct 1–166; UniProt 1–166

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9ya3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9ya3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9ya3
Deposition date deposition_date2025-09-15
Structure title titleCryo-EM structure of the apical region of subpellicular microtubule (SPMT) from Toxoplasma gondii (8-nm repeat)
Keywords keywords;Tubulin, Microtubule, Microtubule Inner Protein, Microtubule-associated Protein, Toxoplasma gondii, conoid, conoid fiber, subpellicular microtubule, SPMT, STRUCTURAL PROTEIN ;; STRUCTURAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier
Radius of gyration Rg (electron density) rg_electron120.50
Forward intensity I(0) i0149597000000.00
Molecular weight molecular_weight3251100.0 kDa
Excluded volume excluded_volume4037400 ų
Envelope volume envelope_volume7064500 ų
Hydration-shell volume shell_volume470050 ų
Envelope diameter envelope_diameter372.6
Shell Rg shell_rg136.40
Envelope Rg envelope_rg110.40
Shape Rg shape_rg120.50
Total Rg total_rg120.60
Total atoms total_atoms228257
Residues n_residues28883
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax338.1
Rg (real space) rg_real121.20
Rg uncertainty (real space) rg_real_error1.15
I(0) (real space) i0_real1.4590e+11
I(0) uncertainty (real space) i0_real_error3.3570e+09
Rg (reciprocal space) rg_reciprocal127.20
I(0) (reciprocal space) i0_reciprocal152600000000.0000
Solution quality estimate total_estimate0.8932
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary182.0
Skewness Skewness skewness-0.135
Kurtosis Kurtosis kurtosis-0.721
Angular range angular_range— – 0.0650 −1
Current regularization parameter α current_alpha1.7570
Highest regularization parameter α highest_alpha3476000000.0000
Real-space data points n_real_points14
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.951; Stabil: 0.930; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (11)

8. Citations (1)

9. Files and Curves (10)