PDB-4igg: Full-length human alpha-catenin crystal structure

ID or keywords:

Entry

Database: PDB / ID: 4igg

Title

Full-length human alpha-catenin crystal structure

Components

Catenin alpha-1

Keywords

CELL ADHESION / Asymmetric dimer / adherens junctions / F-actin binding

Function / homology

Function and homology information

negative regulation of integrin-mediated signaling pathway / CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / Regulation of CDH11 function / gamma-catenin binding / epithelial cell-cell adhesion / zonula adherens / gap junction assembly / cellular response to indole-3-methanol / flotillin complex ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 3.66 Å

Authors

Izard, T. / Rangarajan, E.S.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Dimer asymmetry defines alpha-catenin interactions.
Authors: Rangarajan, E.S. / Izard, T.

History

Deposition	Dec 17, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 26, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 11, 2013	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4igg.cif.gz	299.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4igg.ent.gz	239.9 KB	Display	PDB format
PDBx/mmJSON format	4igg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4igg_validation.pdf.gz	458 KB	Display	wwPDB validaton report
Full document	4igg_full_validation.pdf.gz	481.3 KB	Display
Data in XML	4igg_validation.xml.gz	50.7 KB	Display
Data in CIF	4igg_validation.cif.gz	68.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ig/4igg ftp://data.pdbj.org/pub/pdb/validation_reports/ig/4igg	HTTPS FTP

-
Related structure data

Related structure data	4ehp
Similar structure data	6t0n-d 6gtg-d 5m4y-d 21132 5xuu-d 0670 30284 6tz2-d 30283 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	#134 - Feb 2011 Integrin similarity (1) #231 - Mar 2019 Measles Virus Proteins similarity (1) #245 - May 2020 Spliceosomes similarity (2) #44 - Aug 2003 Calmodulin similarity (2) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #196 - Apr 2016 Lead Poisoning similarity (2) #28 - Apr 2002 Anthrax Toxin similarity (2)

Deposited unit

A: Catenin alpha-1

B: Catenin alpha-1

hetero molecules

185 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	145.629, 145.629, 139.081
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	Catenin alpha-1 / Alpha E-catenin / Cadherin-associated protein / Renal carcinoma antigen NY-REN-13 Mass: 92207.984 Da / Num. of mol.: 2 / Fragment: UNP residues 82-906 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNA1 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P35221
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄

#1: Protein

Catenin alpha-1 / Alpha E-catenin / Cadherin-associated protein / Renal carcinoma antigen NY-REN-13

Mass: 92207.984 Da / Num. of mol.: 2 / Fragment: UNP residues 82-906
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: CTNNA1 / Plasmid: pET24 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P35221

#2: Chemical

ChemComp-PO4 / PHOSPHATE ION

Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.62 Å³/Da / Density % sol: 73.36 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion / pH: 6.8 Details: 0.9 M Na/K Phosphate, 0.3 M Na Malonate, pH 6.8, VAPOR DIFFUSION, temperature 295K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-BM / Wavelength: 1 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2010

Radiation

Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Redundancy: 5.2 % / Av σ(I) over netI: 17 / Number: 52879 / R_sym value: 0.036 / D res high: 5.583 Å / D res low: 46.687 Å / Num. obs: 10122 / % possible obs: 99.4

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Redundancy
17.65	46.69	93.9	1	0.018	0.018	5.2
12.48	17.65	99.1	1	0.021	0.021	4.7
10.19	12.48	99.7	1	0.02	0.02	5.4
8.83	10.19	99.6	1	0.022	0.022	5.3
7.9	8.83	99	1	0.031	0.031	4.8
7.21	7.9	100	1	0.055	0.055	5.3
6.67	7.21	100	1	0.112	0.112	5.5
6.24	6.67	100	1	0.182	0.182	5.5
5.88	6.24	98.9	1	0.294	0.294	5.3
5.58	5.88	99.5	1	0.412	0.412	5

Reflection

Resolution: 3.658→139.081 Å / Num. all: 36415 / Num. obs: 36415 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / B_iso Wilson estimate: 81.83 Å² / R_sym value: 0.077 / Net I/σ(I): 15.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
3.66-3.86	5.8	0.491	1.5	30931	5322	0.491	100
3.86-4.09	5.8	0.282	2.6	29353	5036	0.282	100
4.09-4.37	5.8	0.164	4.5	27703	4738	0.164	100
4.37-4.72	5.8	0.111	6.6	25656	4387	0.111	100
4.72-5.17	5.8	0.086	8.6	23707	4062	0.086	100
5.17-5.78	5.8	0.104	7	21460	3677	0.104	100
5.78-6.68	5.8	0.085	8.8	18840	3225	0.085	100
6.68-8.18	5.7	0.043	15.7	15603	2722	0.043	100
8.18-11.57	5.6	0.029	21.4	11888	2106	0.029	99.6
11.57-139.081	5.3	0.029	20.8	6002	1140	0.029	98.2

-
Phasing

Phasing

Method:

SIRAS

Phasing MAD

D res high: 4.3 Å / D res low: 93.43 Å / FOM acentric: 0.155 / FOM centric: 0 / Reflection acentric: 22395 / Reflection centric: 0

Phasing MAD set

ID	Highest resolution (Å)	Lowest resolution (Å)	Power acentric	Reflection acentric
ISO_1	4.3	93.43	0	22353
ISO_2	4.3	93.43	0.919	9955
ANO_1	4.3	93.43	0	0
ANO_2	4.3	93.43	1.494	9884

Phasing MAD set shell

ID	Resolution (Å)	Power acentric	Reflection acentric
ISO_1	18.86-93.43	0	233
ISO_1	13.47-18.86	0	456
ISO_1	11.04-13.47	0	587
ISO_1	9.58-11.04	0	700
ISO_1	8.57-9.58	0	800
ISO_1	7.83-8.57	0	881
ISO_1	7.25-7.83	0	963
ISO_1	6.79-7.25	0	1033
ISO_1	6.4-6.79	0	1087
ISO_1	6.07-6.4	0	1161
ISO_1	5.79-6.07	0	1205
ISO_1	5.55-5.79	0	1291
ISO_1	5.33-5.55	0	1311
ISO_1	5.14-5.33	0	1389
ISO_1	4.96-5.14	0	1427
ISO_1	4.81-4.96	0	1448
ISO_1	4.66-4.81	0	1545
ISO_1	4.53-4.66	0	1584
ISO_1	4.41-4.53	0	1609
ISO_1	4.3-4.41	0	1643
ANO_1	18.86-93.43	0	0
ANO_1	13.47-18.86	0	0
ANO_1	11.04-13.47	0	0
ANO_1	9.58-11.04	0	0
ANO_1	8.57-9.58	0	0
ANO_1	7.83-8.57	0	0
ANO_1	7.25-7.83	0	0
ANO_1	6.79-7.25	0	0
ANO_1	6.4-6.79	0	0
ANO_1	6.07-6.4	0	0
ANO_1	5.79-6.07	0	0
ANO_1	5.55-5.79	0	0
ANO_1	5.33-5.55	0	0
ANO_1	5.14-5.33	0	0
ANO_1	4.96-5.14	0	0
ANO_1	4.81-4.96	0	0
ANO_1	4.66-4.81	0	0
ANO_1	4.53-4.66	0	0
ANO_1	4.41-4.53	0	0
ANO_1	4.3-4.41	0	0
ISO_2	18.86-93.43	1.13	214
ISO_2	13.47-18.86	1.232	425
ISO_2	11.04-13.47	1.112	577
ISO_2	9.58-11.04	0.828	697
ISO_2	8.57-9.58	0.676	773
ISO_2	7.83-8.57	0.618	869
ISO_2	7.25-7.83	0.589	960
ISO_2	6.79-7.25	0.572	1030
ISO_2	6.4-6.79	0.521	1084
ISO_2	6.07-6.4	0.486	1159
ISO_2	5.79-6.07	0.437	1167
ISO_2	5.55-5.79	0.393	998
ISO_2	5.33-5.55	1.011	2
ISO_2	5.14-5.33	0	0
ISO_2	4.96-5.14	0	0
ISO_2	4.81-4.96	0	0
ISO_2	4.66-4.81	0	0
ISO_2	4.53-4.66	0	0
ISO_2	4.41-4.53	0	0
ISO_2	4.3-4.41	0	0
ANO_2	18.86-93.43	4.776	233
ANO_2	13.47-18.86	4.104	404
ANO_2	11.04-13.47	3.325	576
ANO_2	9.58-11.04	2.878	690
ANO_2	8.57-9.58	2.319	753
ANO_2	7.83-8.57	1.575	860
ANO_2	7.25-7.83	1.037	957
ANO_2	6.79-7.25	0.728	1028
ANO_2	6.4-6.79	0.482	1084
ANO_2	6.07-6.4	0.366	1156
ANO_2	5.79-6.07	0.268	1149
ANO_2	5.55-5.79	0.214	992
ANO_2	5.33-5.55	0.126	2
ANO_2	5.14-5.33	0	0
ANO_2	4.96-5.14	0	0
ANO_2	4.81-4.96	0	0
ANO_2	4.66-4.81	0	0
ANO_2	4.53-4.66	0	0
ANO_2	4.41-4.53	0	0
ANO_2	4.3-4.41	0	0

Phasing MAD shell

Resolution (Å)	FOM acentric	Reflection acentric
18.86-93.43	0.715	258
13.47-18.86	0.692	460
11.04-13.47	0.718	593
9.58-11.04	0.642	703
8.57-9.58	0.521	801
7.83-8.57	0.43	883
7.25-7.83	0.33	963
6.79-7.25	0.259	1033
6.4-6.79	0.218	1087
6.07-6.4	0.17	1161
5.79-6.07	0.132	1205
5.55-5.79	0.087	1292
5.33-5.55	0	1311
5.14-5.33	0	1389
4.96-5.14	0	1427
4.81-4.96	0	1448
4.66-4.81	0	1545
4.53-4.66	0	1584
4.41-4.53	0	1609
4.3-4.41	0	1643

-
Processing

Software

Name	Version	Classification
SCALA	3.3.16	data scaling
SHARP		phasing
SOLOMON		phasing
TNT		refinement
PDB_EXTRACT	3.11	data extraction
SERGUI		data collection
XSCALE		data scaling
BUSTER	2.11.2	refinement

Refinement

Method to determine structure:

SIRAS / Resolution: 3.66→23.21 Å / Cor.coef. F_o:F_c: 0.9274 / Cor.coef. F_o:F_c free: 0.9296 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2413	1821	5.03 %	RANDOM
R_work	0.2175	-	-	-
obs	0.2187	36178	99.93 %	-
all	-	36368	-	-

Displacement parameters

B_iso max: 270.94 Å² / B_iso mean: 126.5886 Å² / B_iso min: 20 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	14.9444 Å²	0 Å²	0 Å²
2-	-	14.9444 Å²	0 Å²
3-	-	-	-29.8887 Å²

Refine analyze

Luzzati coordinate error obs: 1.07 Å

Refinement step

Cycle: LAST / Resolution: 3.66→23.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11704	0	10	0	11714

Refine LS restraints

Refine-ID	Type	Number	Restraint function	Weight	Dev ideal
X-RAY DIFFRACTION	t_dihedral_angle_d	5857	SINUSOIDAL	2
X-RAY DIFFRACTION	t_trig_c_planes	377	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes	1680	HARMONIC	5
X-RAY DIFFRACTION	t_it	11832	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_chiral_improper_torsion	1579	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact	14475	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_bond_d	11832	HARMONIC	2	0.008
X-RAY DIFFRACTION	t_angle_deg	15940	HARMONIC	2	0.99
X-RAY DIFFRACTION	t_omega_torsion				1.96
X-RAY DIFFRACTION	t_other_torsion				3.45

LS refinement shell

Resolution: 3.66→3.77 Å / Total num. of bins used: 18

	R_factor	Num. reflection	% reflection
R_free	0.286	157	5.32 %
R_work	0.2726	2795	-
all	0.2733	2952	-
obs	-	-	99.93 %

-
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

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-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

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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