PDB-7dfc: Crystal of Arrestin2-V2Rpp-3-Fab30 complex

ID or keywords:

Entry

Database: PDB / ID: 7dfc

Title

Crystal of Arrestin2-V2Rpp-3-Fab30 complex

Components

Beta-arrestin-1
FAB30 HEAVY CHAIN
FAB30 LIGHT CHAIN
V2Rpp-3

Keywords

SIGNALING PROTEIN / Arrestin / G-protein-coupled receptor / Phosphopeptide / Antibody fragment

Function / homology

Function and homology information

TGFBR3 regulates TGF-beta signaling / MAP2K and MAPK activation / Activation of SMO / Golgi Associated Vesicle Biogenesis / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / Ub-specific processing proteases / clathrin coat of coated pit / clathrin heavy chain binding / Cargo recognition for clathrin-mediated endocytosis ...
Similarity search - Function

Biological species

Bos taurus (domestic cattle)

Mus musculus (house mouse)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.49 Å

Authors

Sun, J.P. / Yu, X. / Xiao, P. / He, Q.T. / Lin, J.Y. / Zhu, Z.L.

Funding support

China, 1items

Citation

Journal: Nat Commun / Year: 2021
Title: Structural studies of phosphorylation-dependent interactions between the V2R receptor and arrestin-2.
Authors: He, Q.T. / Xiao, P. / Huang, S.M. / Jia, Y.L. / Zhu, Z.L. / Lin, J.Y. / Yang, F. / Tao, X.N. / Zhao, R.J. / Gao, F.Y. / Niu, X.G. / Xiao, K.H. / Wang, J. / Jin, C. / Sun, J.P. / Yu, X.

History

Deposition	Nov 6, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 28, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7dfc.cif.gz	361.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7dfc.ent.gz	261.4 KB	Display	PDB format
PDBx/mmJSON format	7dfc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7dfc_validation.pdf.gz	718.2 KB	Display	wwPDB validaton report
Full document	7dfc_full_validation.pdf.gz	735.2 KB	Display
Data in XML	7dfc_validation.xml.gz	30.9 KB	Display
Data in CIF	7dfc_validation.cif.gz	42.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/df/7dfc ftp://data.pdbj.org/pub/pdb/validation_reports/df/7dfc	HTTPS FTP

-
Related structure data

Related structure data	7df9C 7dfaC 7dfbC 4jqiS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7dfb-d 7dfa-d 7df9-d 4jqi-d 4f15-4 6cxy-d 4m6a-d 6nmg-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #164 - Aug 2013 Serotonin Receptor similarity (1) #58 - Oct 2004 G Proteins similarity (1)

Deposited unit

A: Beta-arrestin-1

V: V2Rpp-3

L: FAB30 LIGHT CHAIN

H: FAB30 HEAVY CHAIN

hetero molecules

103 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	116.137, 122.653, 144.064
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	24
Space group name H-M	I2₁2₁2₁
Space group name Hall	I2b2c
Symmetry operation	#1: x,y,z #2: x,-y,-z+1/2 #3: -x+1/2,y,-z #4: -x,-y+1/2,z #5: x+1/2,y+1/2,z+1/2 #6: x+1/2,-y+1/2,-z+1 #7: -x+1,y+1/2,-z+1/2 #8: -x+1/2,-y+1,z+1/2

-
Antibody , 2 types, 2 molecules LH

#3: Antibody	FAB30 LIGHT CHAIN Mass: 24751.596 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#4: Antibody	FAB30 HEAVY CHAIN Mass: 26828.885 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

-
Protein / Protein/peptide , 2 types, 2 molecules AV

#1: Protein	Beta-arrestin-1 / Arrestin beta-1 / Arrestin-2 Mass: 48272.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ARRB1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P17870
#2: Protein/peptide	V2Rpp-3 Mass: 2881.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 2 types, 58 molecules

#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.51 Å³/Da / Density % sol: 50.92 %
Crystal grow	Temperature: 289 K / Method: evaporation / pH: 7.5 / Details: 15% PEG 3350, 0.1M HEPES, 0.2mM DMSO

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.05 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.05 Å / Relative weight: 1
Reflection	Resolution: 2.45→46.69 Å / Num. obs: 38166 / % possible obs: 99.6 % / Redundancy: 7.2 % / B_iso Wilson estimate: 60.49 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.062 / R_pim(I) all: 0.025 / Net I/σ(I): 18.5
Reflection shell	Resolution: 2.45→2.55 Å / R_merge(I) obs: 0.959 / Num. unique obs: 4165 / CC_1/2: 0.85 / R_pim(I) all: 0.548

-
Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4JQI

4jqi

Resolution: 2.49→46.69 Å / SU ML: 0.3759 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.3846 / Stereochemistry target values: CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.284	1892	5.2 %
R_work	0.2285	34493	-
obs	0.2315	36385	99.55 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 88.3 Å²

Refinement step

Cycle: LAST / Resolution: 2.49→46.69 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5915	0	6	57	5978

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0091	6053
X-RAY DIFFRACTION	f_angle_d	1.1588	8271
X-RAY DIFFRACTION	f_chiral_restr	0.0679	963
X-RAY DIFFRACTION	f_plane_restr	0.0073	1053
X-RAY DIFFRACTION	f_dihedral_angle_d	21.2685	2141

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.49-2.55	0.4124	140	0.3384	2388	X-RAY DIFFRACTION	98.63
2.55-2.62	0.3468	142	0.3133	2407	X-RAY DIFFRACTION	99.07
2.62-2.69	0.3524	122	0.2908	2459	X-RAY DIFFRACTION	99.69
2.69-2.78	0.3099	149	0.2699	2443	X-RAY DIFFRACTION	99.69
2.78-2.88	0.3431	128	0.2722	2421	X-RAY DIFFRACTION	99.61
2.88-3	0.4452	116	0.2837	2491	X-RAY DIFFRACTION	99.69
3-3.13	0.3367	137	0.2841	2422	X-RAY DIFFRACTION	99.77
3.13-3.3	0.3555	120	0.269	2480	X-RAY DIFFRACTION	99.88
3.3-3.5	0.343	130	0.2543	2463	X-RAY DIFFRACTION	99.81
3.5-3.77	0.3192	141	0.2401	2448	X-RAY DIFFRACTION	99.81
3.77-4.15	0.3092	114	0.2211	2506	X-RAY DIFFRACTION	99.81
4.15-4.75	0.2192	152	0.1792	2475	X-RAY DIFFRACTION	99.85
4.75-5.99	0.2235	160	0.1958	2494	X-RAY DIFFRACTION	99.89
5.99-46.7	0.2522	141	0.2055	2596	X-RAY DIFFRACTION	98.63

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.1931586594	-0.825405194441	0.792582862953	3.55146647409	-0.657139527961	0.548557650531	0.151073939781	0.345719078818	0.19468864573	-0.190718663934	-0.422554619324	-0.38359398518	-1.33009749579	0.0234605500225	0.252401436109	1.38670581763	0.279285339834	0.0894674685167	0.473751728532	0.152798429709	0.541079132056	12.7975561386	21.0803231625	-1.87527395642
2	1.61337267145	-0.859266183045	0.554446444291	0.661726398767	-0.990315513226	3.95389038412	0.0103043210929	0.151608600373	0.381673158247	0.0901110010112	-0.330317183599	-0.517896295763	-1.40055310363	0.700895765622	0.260564382231	1.28641888292	0.0213312292088	0.0530458633298	0.41536837779	0.176599222153	0.695370204233	21.3253601079	20.3507748391	-4.57838821484
3	2.04314914977	-1.81836841892	0.243596637059	5.23186959577	-1.48123862938	1.00119676781	0.207269425442	0.235595209921	0.500336673068	0.243053911956	-0.533750998115	-0.0995469373724	-1.22499858705	-0.173435171366	0.224668487529	1.42926382436	0.254448505359	-0.0227143477947	0.46741948241	-0.00577498362237	0.489773547413	11.1796117028	17.2450364088	3.99353380436
4	1.6113041005	-0.305266368195	-1.25173749581	2.42249805243	-2.0010462257	5.68544054625	-0.00845852986977	-0.0145184601544	-0.242266732894	0.644352060605	-0.341697052757	-0.0131402207171	0.737852562912	-0.531432035162	0.320723083123	0.842620796038	-0.0647035257036	0.00632988931358	0.361649568411	-0.0495878492981	0.374726754718	6.74648549945	-12.7624797284	25.9568873003
5	2.79992123097	0.861021723381	-1.60030306032	5.17896372296	-2.64356381612	6.00245800246	0.172326125228	0.449818238548	0.212310033431	-0.0260443722174	-0.324433147424	-0.111577508634	-0.797206904523	-0.401180350074	0.164922360524	0.622115858073	0.10810068518	-0.00959780261351	0.307297734432	-0.0624943296191	0.259967418636	5.84807880243	2.45690853367	14.4743433534
6	3.41263900158	0.206718290675	-1.19264717615	2.60123877315	1.65698693405	1.43089703905	0.0479031630861	0.496141980386	0.0812931406397	0.0194370809997	-0.333848950527	0.0265603905266	-0.16063164842	-0.423060084272	0.163217098768	0.562738295829	-0.00981079182599	0.026788977597	0.252580427121	-0.0619871788266	0.382232354343	6.84859334652	-5.3078126291	18.2216862579
7	3.6416862248	-3.41048376656	-3.3943949885	5.47269808197	5.46210526996	5.29732812766	0.0488342714262	0.47268698988	0.0997503566478	-0.198285953542	-0.710647992372	0.393505386311	-0.93029307854	-0.431341987113	0.435937298749	1.37074018833	0.284172230188	0.0233189468524	0.708561962069	0.0990070989385	0.509892936247	6.37560508354	21.4046388854	-4.35323057045
8	1.32206883103	0.949341724455	1.22178347455	1.35488668667	0.715671878772	1.36939390945	-0.550603351742	0.95987723298	-0.14555849015	-0.517404693749	0.419890177779	-0.477005056487	0.021768709948	-1.53873853525	0.0174345129504	0.975626136342	-0.0772065258311	0.221821722031	1.65659890899	-0.205350118562	0.383531807138	-1.36957839326	-5.02559494337	-24.1722926032
9	5.38533888036	1.21407815417	-0.589247435245	3.24885512117	1.20190407522	8.90193017325	-0.845974617949	1.15082791015	-0.367186095858	-0.759300445088	0.290213113232	0.22438515582	-0.0863114335331	-0.0360748963924	0.550251199751	0.99852272537	-0.204097940487	0.0561302714376	0.675610128588	-0.0846011244861	0.574521217615	-26.133464601	-22.7436829783	-41.3588985852
10	1.07396889156	1.05588552721	1.38185640045	1.86490481558	1.07705338435	2.48180551949	-0.26941509484	0.895485006769	-0.588527978086	-0.288573645664	0.247260923625	-0.433520753497	0.142300060563	-2.44850844383	-0.160096800652	0.771095298285	-0.0129776097124	-0.0132206458139	2.52084270128	-0.159003487946	0.0139613269841	-15.5510934041	-8.45940430583	-4.16916873042
11	2.77916263926	2.07173406646	3.57579967709	1.84724966319	2.40270332503	3.67126856993	0.498603871297	-1.01169389542	-0.489813171876	0.0940097433269	-0.27589541913	-0.133254332976	0.733869172522	-1.04724804644	-0.204225291376	0.957221904808	-0.0629651713106	-0.0159091852867	1.54780074516	-0.0879538234239	0.521498061349	-15.5447482794	-17.4390828913	-16.9568021857
12	4.2836180465	0.126120674772	1.70787358965	0.518293495693	-1.74088632915	7.07845822556	0.486904643944	-2.16066137532	-1.78702810257	-0.687410428114	-0.321532972606	-0.650111631186	1.15618470434	-0.141060842616	-0.153359851583	1.2103082861	-0.269614158973	0.094426617532	1.06546539155	0.154056090977	1.02405281222	-22.1463250836	-31.2601740432	-27.1929827106
13	5.68064289169	-0.458575116959	6.52946568717	8.89763316168	-3.0296655627	8.22262288476	0.469928905059	-1.18351897004	-0.549872387062	1.51533947488	-0.169293741979	0.307845675379	0.541787431584	0.706587253955	-0.302186371663	1.03839260808	-0.169994846184	0.0585811156001	1.18595762191	-0.0626568527755	0.544764519942	-23.728261894	-30.1542894238	-27.5930599127

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 74 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 75 through 129 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 130 through 182 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 183 through 274 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 275 through 329 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 330 through 367 )
7	X-RAY DIFFRACTION	7	chain 'V' and (resid 346 through 367 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 14 through 126 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 127 through 224 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 17 through 106 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 107 through 156 )
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 157 through 184 )
13	X-RAY DIFFRACTION	13	chain 'H' and (resid 185 through 234 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Antibody , 2 types, 2 molecules LH

-
Protein / Protein/peptide , 2 types, 2 molecules AV

-
Non-polymers , 2 types, 58 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Antibody , 2 types, 2 molecules LH

-Protein / Protein/peptide , 2 types, 2 molecules AV

-Non-polymers , 2 types, 58 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Antibody , 2 types, 2 molecules LH

-
Protein / Protein/peptide , 2 types, 2 molecules AV

-
Non-polymers , 2 types, 58 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi