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2vbl

Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers

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

DNA ENDONUCLEASE I-CREI

CHLAMYDOMONAS REINHARDTII

UniProt P05725

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Homooligomer Protein 2 DNA 4 ;5'-D(*DT*DC*DT*DG*DC*DC*DT*DT*DT*DT*DT*DT *DGP*DAP)-3' ; × 1 ;5'-D(*DT*DT*DA*DG*DG*DA*DT*DC*DC*DT*DT*DC *DAP*DAP)-3' ; × 1 5'-D(*DA*DA*DA*DA*DG*DG*DC*DA*DG*DAP)-3' × 1 5'-D(*DA*DG*DG*DA*DT*DC*DC*DT*DA*DAP)-3' × 1 MAGNESIUM ION × 3 water × 6 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1af5 2o7m

2 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1bp7 1bp7 1g9y 1g9z 1n3e 1n3e 1n3f 1n3f 1t9i 1t9j 1u0c 1u0d

29 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DNE1_CHLRE
Isoform —
PDB entities 1, 2
Chains and sequence ranges Author chain A； PDBConstruct 1–153； UniProt 1–153 Author chain B； PDBConstruct 1–153； UniProt 1–153

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_id2vbl
Deposition date deposition_date2007-09-14
Structure title titleMolecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers
Keywords keywords;UV-INDUCED DNA DAMAGE, CUTTING DNA ENDONUCLEASES, PLASTID, NUCLEASE, HYDROLASE, CHLOROPLAST, ENDONUCLEASE, INTRON HOMING, AMEL3- 4_MAGNESIUM, DOUBLE STRAND BREAK (DSB), HOMING ENDONUCLEASES (HES) ;; HYDROLASE
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.

2vbl__assembly_1__model_1

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

Download this curve (.dat)

2vbl__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2vbl__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）24.80 Å
Rg (electron density)24.17 Å
Total Rg24.92 Å
Atom count3431
Residues352
Excluded volume58607 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2vbl__assembly_1__model_1 hexameric （6） 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 (8)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2vbla_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.95 — Homing endonuclease-like
Superfamily Superfamily superfamilyd.95.2 — Homing endonucleases
Family Family familyd.95.2.1 — Group I mobile intron endonuclease
Domain ID domain_idd2vblb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.95 — Homing endonuclease-like
Superfamily Superfamily superfamilyd.95.2 — Homing endonucleases
Family Family familyd.95.2.1 — Group I mobile intron endonuclease

CATH v4.4 (2 domains)

Domain ID domain_id2vblA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology28 — Endonuclease I-creI
Homologous superfamily homologous superfamily10 — Homing endonucleases
Domain ID domain_id2vblB00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology28 — Endonuclease I-creI
Homologous superfamily homologous superfamily10 — Homing endonucleases
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7. Citations (1)