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4rbo

Crystal structure of a Nanog homeobox (NANOG) from Homo sapiens at 3.30 A resolution

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

Putative homeobox protein NANOGP8

Homo sapiens

UniProt Q6NSW7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*GP*GP*CP*CP*CP*AP*TP*TP*CP*AP*AP*G)-3' × 1 5'-D(*CP*TP*TP*GP*AP*AP*TP*GP*GP*GP*CP*C)-3' × 1 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*GP*GP*CP*CP*CP*AP*TP*TP*CP*AP*AP*G)-3' × 1 5'-D(*CP*TP*TP*GP*AP*AP*TP*GP*GP*GP*CP*C)-3' × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
2kt0

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4rbo 4rbo

2 assemblies

View Construct and Data Evidence
UniProt name NANP8_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–70； UniProt 94–162 Author chain D； PDBConstruct 2–70； UniProt 94–162

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_id4rbo
Deposition date deposition_date2014-09-12
Structure title titleCrystal structure of a Nanog homeobox (NANOG) from Homo sapiens at 3.30 A resolution
Keywords keywords;Homeobox, PF00046 family, Structural Genomics, Joint Center for Structural Genomics, JCSG, Partnership for Stem Cell Biology, STEMCELL, Protein Structure Initiative, PSI-BIOLOGY, DNA BINDING PROTEIN, TRANSCRIPTION, TRANSCRIPTION-DNA complex ;; DNA BINDING PROTEIN, TRANSCRIPTION/DNA
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.

4rbo__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4rbo__assembly_2__model_1 | I(q)

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

4rbo__assembly_2__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）15.33 Å
Rg (electron density)14.35 Å
Total Rg15.33 Å
Atom count1671
Residues78
Excluded volume15196 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4rbo__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4rbo__assembly_2__model_1 trimeric （3） 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 (3)

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4rboA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id4rboD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
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7. Citations (1)