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4d0m

Phosphatidylinositol 4-kinase III beta in a complex with Rab11a-GTP- gamma-S and the Rab-binding domain of FIP3

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHOSPHATIDYLINOSITOL 4-KINASE BETA

HOMO SAPIENS

UniProt Q9UBF8

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 12 RAS-RELATED PROTEIN RAB-11A × 4 （P62491） RAB11 FAMILY-INTERACTING PROTEIN 3 × 4 （O75154） N-(5-(4-CHLORO-3-(2-HYDROXY-ETHYLSULFAMOYL)- PHENYLTHIAZOLE-2-YL)-ACETAMIDE × 4 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 4 MAGNESIUM ION × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 12 RAS-RELATED PROTEIN RAB-11A × 4 （P62491） RAB11 FAMILY-INTERACTING PROTEIN 3 × 4 （O75154） N-(5-(4-CHLORO-3-(2-HYDROXY-ETHYLSULFAMOYL)- PHENYLTHIAZOLE-2-YL)-ACETAMIDE × 4 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 4 MAGNESIUM ION × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 12 RAS-RELATED PROTEIN RAB-11A × 4 （P62491） RAB11 FAMILY-INTERACTING PROTEIN 3 × 4 （O75154） N-(5-(4-CHLORO-3-(2-HYDROXY-ETHYLSULFAMOYL)- PHENYLTHIAZOLE-2-YL)-ACETAMIDE × 4 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 4 MAGNESIUM ION × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
4wae 4wag 6gl3 6gl3

4 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4d0l 4d0l 4d0l 4d0m 4d0m 4d0m 5c46 5c4g 5euq 5fbl 5fbq 5fbr

19 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name PI4KB_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–185； UniProt 121–303 Author chain A； PDBConstruct 186–288； UniProt 319–421 Author chain A； PDBConstruct 289–566； UniProt 522–799 Author chain C； PDBConstruct 3–185； UniProt 121–303 Author chain C； PDBConstruct 186–288； UniProt 319–421 Author chain C； PDBConstruct 289–566； UniProt 522–799 Author chain G； PDBConstruct 3–185； UniProt 121–303 Author chain G； PDBConstruct 186–288； UniProt 319–421 Author chain G； PDBConstruct 289–566； UniProt 522–799 Author chain I； PDBConstruct 3–185； UniProt 121–303 Author chain I； PDBConstruct 186–288； UniProt 319–421 Author chain I； PDBConstruct 289–566； UniProt 522–799 Author chain M； PDBConstruct 3–185； UniProt 121–303 Author chain M； PDBConstruct 186–288； UniProt 319–421 Author chain M； PDBConstruct 289–566； UniProt 522–799 Author chain O； PDBConstruct 3–185； UniProt 121–303 Author chain O； PDBConstruct 186–288； UniProt 319–421 Author chain O； PDBConstruct 289–566； UniProt 522–799 Author chain Q； PDBConstruct 3–185； UniProt 121–303 Author chain Q； PDBConstruct 186–288； UniProt 319–421 Author chain Q； PDBConstruct 289–566； UniProt 522–799 Author chain S； PDBConstruct 3–185； UniProt 121–303 Author chain S； PDBConstruct 186–288； UniProt 319–421 Author chain S； PDBConstruct 289–566； UniProt 522–799 Author chain W； PDBConstruct 3–185； UniProt 121–303 Author chain W； PDBConstruct 186–288； UniProt 319–421 Author chain W； PDBConstruct 289–566； UniProt 522–799 Author chain Y； PDBConstruct 3–185； UniProt 121–303 Author chain Y； PDBConstruct 186–288； UniProt 319–421 Author chain Y； PDBConstruct 289–566； UniProt 522–799 Author chain c； PDBConstruct 3–185； UniProt 121–303 Author chain c； PDBConstruct 186–288； UniProt 319–421 Author chain c； PDBConstruct 289–566； UniProt 522–799 Author chain g； PDBConstruct 3–185； UniProt 121–303 Author chain g； PDBConstruct 186–288； UniProt 319–421 Author chain g； PDBConstruct 289–566； UniProt 522–799

RAS-RELATED PROTEIN RAB-11A

HOMO SAPIENS

UniProt P62491

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 12 PHOSPHATIDYLINOSITOL 4-KINASE BETA × 4 （Q9UBF8） RAB11 FAMILY-INTERACTING PROTEIN 3 × 4 （O75154） N-(5-(4-CHLORO-3-(2-HYDROXY-ETHYLSULFAMOYL)- PHENYLTHIAZOLE-2-YL)-ACETAMIDE × 4 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 4 MAGNESIUM ION × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 12 PHOSPHATIDYLINOSITOL 4-KINASE BETA × 4 （Q9UBF8） RAB11 FAMILY-INTERACTING PROTEIN 3 × 4 （O75154） N-(5-(4-CHLORO-3-(2-HYDROXY-ETHYLSULFAMOYL)- PHENYLTHIAZOLE-2-YL)-ACETAMIDE × 4 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 4 MAGNESIUM ION × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 12 PHOSPHATIDYLINOSITOL 4-KINASE BETA × 4 （Q9UBF8） RAB11 FAMILY-INTERACTING PROTEIN 3 × 4 （O75154） N-(5-(4-CHLORO-3-(2-HYDROXY-ETHYLSULFAMOYL)- PHENYLTHIAZOLE-2-YL)-ACETAMIDE × 4 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 4 MAGNESIUM ION × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1yzk 6iy1 6iy1 6iy1 6iy1 6iy1 6iy1

7 assemblies

Homodimer
5ez5 5ez5

2 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2d7c 2d7c 2gzd 2gzh 2hv8 2hv8 4c4p 4d0l 4d0l 4d0l 4d0m 4d0m

50 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RB11A_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 4–219； UniProt 1–216 Author chain D； PDBConstruct 4–219； UniProt 1–216 Author chain H； PDBConstruct 4–219； UniProt 1–216 Author chain J； PDBConstruct 4–219； UniProt 1–216 Author chain N； PDBConstruct 4–219； UniProt 1–216 Author chain P； PDBConstruct 4–219； UniProt 1–216 Author chain R； PDBConstruct 4–219； UniProt 1–216 Author chain T； PDBConstruct 4–219； UniProt 1–216 Author chain X； PDBConstruct 4–219； UniProt 1–216 Author chain Z； PDBConstruct 4–219； UniProt 1–216 Author chain d； PDBConstruct 4–219； UniProt 1–216 Author chain h； PDBConstruct 4–219； UniProt 1–216

RAB11 FAMILY-INTERACTING PROTEIN 3

HOMO SAPIENS

UniProt O75154

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 12 PHOSPHATIDYLINOSITOL 4-KINASE BETA × 4 （Q9UBF8） RAS-RELATED PROTEIN RAB-11A × 4 （P62491） N-(5-(4-CHLORO-3-(2-HYDROXY-ETHYLSULFAMOYL)- PHENYLTHIAZOLE-2-YL)-ACETAMIDE × 4 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 4 MAGNESIUM ION × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 12 PHOSPHATIDYLINOSITOL 4-KINASE BETA × 4 （Q9UBF8） RAS-RELATED PROTEIN RAB-11A × 4 （P62491） N-(5-(4-CHLORO-3-(2-HYDROXY-ETHYLSULFAMOYL)- PHENYLTHIAZOLE-2-YL)-ACETAMIDE × 4 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 4 MAGNESIUM ION × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 12 PHOSPHATIDYLINOSITOL 4-KINASE BETA × 4 （Q9UBF8） RAS-RELATED PROTEIN RAB-11A × 4 （P62491） N-(5-(4-CHLORO-3-(2-HYDROXY-ETHYLSULFAMOYL)- PHENYLTHIAZOLE-2-YL)-ACETAMIDE × 4 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 4 MAGNESIUM ION × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2d7c 2d7c 2hv8 2hv8 4d0m 4d0m 4d0m 4uj3 4uj3 4uj3 4uj3 4uj3

18 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RFIP3_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain E； PDBConstruct 5–48； UniProt 713–756 Author chain F； PDBConstruct 5–48； UniProt 713–756 Author chain K； PDBConstruct 5–48； UniProt 713–756 Author chain L； PDBConstruct 5–48； UniProt 713–756 Author chain U； PDBConstruct 5–48； UniProt 713–756 Author chain V； PDBConstruct 5–48； UniProt 713–756 Author chain a； PDBConstruct 5–48； UniProt 713–756 Author chain b； PDBConstruct 5–48； UniProt 713–756 Author chain e； PDBConstruct 5–48； UniProt 713–756 Author chain f； PDBConstruct 5–48； UniProt 713–756 Author chain i； PDBConstruct 5–48； UniProt 713–756 Author chain j； PDBConstruct 5–48； UniProt 713–756

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_id4d0m
Deposition date deposition_date2014-04-29
Structure title titlePhosphatidylinositol 4-kinase III beta in a complex with Rab11a-GTP- gamma-S and the Rab-binding domain of FIP3
Keywords keywords;PHOSPHOINOSITIDE, PHOSPHATIDYLINOSITOL 4-KINASE, LIPID KINASE, FAMILY OF RAB INTERACTING PROTEINS, FIP3, RAB-BINDING DOMAIN, RBD, RAB11, GTP, PIK93, GOLGI, RECYCLING ENDOSOME, SIGNALING PROTEIN ;; SIGNALING PROTEIN
Experimental Method methodX-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.

4d0m__assembly_1__model_1

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

Download this curve (.dat)

4d0m__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4d0m__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）46.45 Å
Rg (electron density)45.85 Å
Total Rg45.99 Å
Atom count21990
Residues2718
Excluded volume393200 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4d0m__assembly_1__model_1 dodecameric （12） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4d0m__assembly_2__model_1 dodecameric （12） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 4d0m__assembly_3__model_1 dodecameric （12） 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 (6)

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7. Citations (1)