8B8I | pdb_00008b8i

Nanobody (NbLumSyt1) bound to human Syt1

PDB DOI: https://doi.org/10.2210/pdb8B8I/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Vicugna pacos, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-10-04 Released: 2024-04-17
Deposition Author(s): Liu, H., Scaletti, E., Stenmark, P.
Funding Organization(s): Swedish Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.298 (Depositor), 0.303 (DCC)
R-Value Work:
0.263 (Depositor), 0.283 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8B8I

This is version 1.2 of the entry. See complete history.

Literature

Nanobody (NbLumSyt1) bound to human Syt1

Liu, H., Scaletti, E., Stenmark, P.

To be published.

Macromolecule Content

Total Structure Weight: 152.48 kDa
Atom Count: 7,778
Modeled Residue Count: 1,052
Deposited Residue Count: 1,424
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody (NbLumSyt1)	A, B, C, D, E A, B, C, D, E, F, G, H	118	Vicugna pacos	Mutation(s): 0

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptotagmin-1	I, J, K, L, M I, J, K, L, M, N, O, P	60	Homo sapiens	Mutation(s): 0 Gene Names: SYT1, SVP65, SYT
UniProt & NIH Common Fund Data Resources
Find proteins for P21579 (Homo sapiens) Explore P21579 Go to UniProtKB: P21579
PHAROS: P21579 GTEx: ENSG00000067715
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21579
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.298 (Depositor), 0.303 (DCC)
R-Value Work: 0.263 (Depositor), 0.283 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.955	α = 90
b = 100.226	β = 100.832
c = 103.939	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	--

Revision History (Full details and data files)

Version 1.0: 2024-04-17
Type: Initial release
Version 1.1: 2024-11-20
Changes: Structure summary
Version 1.2: 2026-03-04
Changes: Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.