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4kml

Probing the N-terminal beta-sheet conversion in the crystal structure of the full-length human prion protein bound to a Nanobody

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

Major prion protein

Homo sapiens

UniProt P04156

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Nanobody × 1 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1fkc 1fo7 1h0l 1hjm 1hjn 1oeh 1oei 1qlx 1qlz 1qm0 1qm1 1qm2

43 assemblies; showing the first 12

Homodimer
1i4m 3haf 3heq 3her 3hes 3hj5 3hjx 3hjx 3md4 3md5

10 assemblies

Homotetramer
6du9

1 assemblies

Other homooligomers
3nhc 3nhd 3nvf 4e1h 4e1i 6lni 6pq5 6pqa 6uur 7dwv 7rl4 7umq

13 assemblies; showing the first 12

Heteromeric or nucleic-acid complex
2w9e 4dgi 4kml 4n9o 6suz 6sv2

6 assemblies

View Construct and Data Evidence
UniProt name PRIO_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 34–241； UniProt 24–231

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_id4kml
Deposition date deposition_date2013-05-08
Structure title titleProbing the N-terminal beta-sheet conversion in the crystal structure of the full-length human prion protein bound to a Nanobody
Keywords keywordsPrion-like fold, antibody, nanobody, MEMBRANE PROTEIN-PROTEIN BINDING complex; MEMBRANE PROTEIN/PROTEIN BINDING
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.

4kml__assembly_1__model_1

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

Download this curve (.dat)

4kml__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.

4kml__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）20.25 Å
Rg (electron density)19.40 Å
Total Rg20.21 Å
Atom count1823
Residues232
Excluded volume31833 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4kml__assembly_1__model_1 dimeric （2） 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) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4kmlb1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd4kmlb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id4kmlB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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7. Citations (1)