9EIU

Crystal structure of the human Cavin1 HR1 TS/DD mutant domain bound to nanobody B7

PDB DOI: https://doi.org/10.2210/pdb9EIU/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Homo sapiens, Vicugna pacos
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-11-26 Released: 2025-02-26
Deposition Author(s): Collins, B.M., Gao, Y.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.00 Å
R-Value Free:
0.264 (Depositor), 0.280 (DCC)
R-Value Work:
0.203 (Depositor), 0.217 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the human Cavin1 HR1 domain bound to nanobody B7

Collins, B.M., Gao, Y.

To be published.

Macromolecule Content

Total Structure Weight: 26.28 kDa
Atom Count: 1,211
Modelled Residue Count: 157
Deposited Residue Count: 237
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caveolae-associated protein 1	A	116	Homo sapiens	Mutation(s): 2 Gene Names: CAVIN1, PTRF, FKSG13
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NZI2 (Homo sapiens) Explore Q6NZI2 Go to UniProtKB: Q6NZI2
PHAROS: Q6NZI2 GTEx: ENSG00000177469
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6NZI2
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody B7	B	121	Vicugna pacos	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.00 Å
R-Value Free: 0.264 (Depositor), 0.280 (DCC)
R-Value Work: 0.203 (Depositor), 0.217 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.669	α = 90
b = 58.669	β = 90
c = 61.293	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-02-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History (Full details and data files)

Version 1.0: 2025-02-26
Type: Initial release

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.