PDB-7w7r: High resolution structure of a fish aquaporin reveals a novel ext...

ID or keywords:

Entry

Database: PDB / ID: 7w7r

Title

High resolution structure of a fish aquaporin reveals a novel extracellular fold.

Components

Aquaporin 1

Keywords

MEMBRANE PROTEIN / Aquaporin / fish / Anabas testudineus / Pichia pastoris / transport protein

Function / homology

Function and homology information

renal water transport / carbon dioxide transmembrane transporter activity / glycerol transmembrane transporter activity / water channel activity / ammonium channel activity / hyperosmotic response / membrane
Similarity search - Function

Biological species

Anabas testudineus (climbing perch)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.46 Å

Authors

Zeng, J. / Schmitz, F. / Isaksson, S. / Glas, J. / Arbab, O. / Andersson, M. / Sundell, K. / Eriksson, L. / Swaminathan, K. / Tornroth-Horsefield, S. / Hedfalk, K.

Funding support

Sweden,

Singapore, 6items

Organization	Grant number	Country
Swedish Research Council	K2013-66X-20431-07-05	Sweden
Swedish Research Council	2009-00360	Sweden
Swedish Research Council	2013-05945	Sweden
Ministry of Education (MoE, Singapore)	R154-000-632-112	Singapore
National Research Foundation (NRF, Singapore)	R706-000-041-279	Singapore
Swedish Research Council FORMAS	2012-771	Sweden

Citation

Journal: Life Sci Alliance / Year: 2022
Title: High-resolution structure of a fish aquaporin reveals a novel extracellular fold.
Authors: Zeng, J. / Schmitz, F. / Isaksson, S. / Glas, J. / Arbab, O. / Andersson, M. / Sundell, K. / Eriksson, L.A. / Swaminathan, K. / Tornroth-Horsefield, S. / Hedfalk, K.

History

Deposition	Dec 6, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 12, 2022	Provider: repository / Type: Initial release
Revision 1.1	Apr 26, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7w7r.cif.gz	340.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7w7r.ent.gz	284.6 KB	Display	PDB format
PDBx/mmJSON format	7w7r.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7w7r_validation.pdf.gz	470.1 KB	Display	wwPDB validaton report
Full document	7w7r_full_validation.pdf.gz	494.5 KB	Display
Data in XML	7w7r_validation.xml.gz	31.2 KB	Display
Data in CIF	7w7r_validation.cif.gz	41.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w7/7w7r ftp://data.pdbj.org/pub/pdb/validation_reports/w7/7w7r	HTTPS FTP

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Related structure data

Related structure data	7w7sC 1j4nS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#173 - May 2014 Aquaporin similarity (7)

Deposited unit

A: Aquaporin 1

B: Aquaporin 1

C: Aquaporin 1

D: Aquaporin 1

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

1

A: Aquaporin 1

C: Aquaporin 1

A: Aquaporin 1

C: Aquaporin 1

defined by author&software
Evidence: gel filtration
102 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Aquaporin 1

D: Aquaporin 1

B: Aquaporin 1

D: Aquaporin 1

defined by author&software
102 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	113.670, 178.100, 177.900
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Aquaporin 1 / Aquaporin 1aa Mass: 25551.859 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anabas testudineus (climbing perch) / Gene: aqp1aa, aqp1 / Production host: Komagataella pastoris (fungus) / References: UniProt: M1K561

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.4 Å³/Da / Density % sol: 72.08 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: reservoir solution: 0.3M Lithium sulfate, 0.1M ADA (pH 6.5), 30% v/v PEG 400. Prior to setting up the crystallization drops, 4 micro liter of the reservoir solution was mixed with 1 micro ...Details: reservoir solution: 0.3M Lithium sulfate, 0.1M ADA (pH 6.5), 30% v/v PEG 400. Prior to setting up the crystallization drops, 4 micro liter of the reservoir solution was mixed with 1 micro liter 30% w/v Dextran sulfate sodium salt Mr 5000. Crystallization drops were set up by mixing the reservoir/additive mixture with protein at 1:1 or 2:1 ratio and the drops were left to equilibrate against 0.5 milliliter reservoir at room temperature and crystal grew in cold room (4 degree)

Crystal

Density Matthews: 4.4 Å³/Da / Density % sol: 72.08 %

Crystal grow

Temperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: reservoir solution: 0.3M Lithium sulfate, 0.1M ADA (pH 6.5), 30% v/v PEG 400. Prior to setting up the crystallization drops, 4 micro liter of the reservoir solution was mixed with 1 micro ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID30B / Wavelength: 0.911647 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 4, 2016

Radiation

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

Radiation wavelength

Wavelength: 0.911647 Å / Relative weight: 1

Reflection

Resolution: 3.46→95.818 Å / Num. all: 23598 / Num. obs: 23598 / % possible obs: 98.8 % / Redundancy: 4.5 % / B_iso Wilson estimate: 89.09 Å² / R_pim(I) all: 0.095 / R_rim(I) all: 0.202 / R_sym value: 0.177 / Net I/av σ(I): 0.6 / Net I/σ(I): 4.5 / Num. measured all: 107214

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique obs	R_pim(I) all	R_rim(I) all	R_sym value	Net I/σ(I) obs	% possible all
3.46-3.65	4.3	0.832	0.9	14473	3367	0.432	0.942	0.832	1.3	97.9
3.65-3.87	4.8	0.655	1.1	15646	3253	0.326	0.734	0.655	1.7	99.7
3.87-4.14	4.7	0.369	1.9	14342	3069	0.184	0.414	0.369	2.7	99.8
4.14-4.47	4.4	0.251	2.7	12229	2802	0.128	0.283	0.251	3.5	98.5
4.47-4.89	4.7	0.155	3.8	12207	2621	0.077	0.174	0.155	4.8	99.3
4.89-5.47	4.7	0.15	4.2	11293	2390	0.073	0.168	0.15	5.3	99.1
5.47-6.32	4.4	0.161	4.1	9224	2079	0.081	0.182	0.161	5.6	97.6
6.32-7.74	4.7	0.104	5.3	8536	1814	0.052	0.117	0.104	8.3	99.3
7.74-10.94	4.3	0.051	8.7	5911	1389	0.028	0.058	0.051	11.3	97.7
10.94-95.818	4.1	0.089	0.8	3353	814	0.068	0.114	0.089	12.9	97.4

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Processing

Software

Name	Version	Classification
SCALA	3.3.22	data scaling
PHENIX	1.10.1_2155	refinement
PDB_EXTRACT	3.25	data extraction
iMOSFLM		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1J4N

1j4n

Resolution: 3.46→84.36 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 40.41 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2991	1060	5.01 %
R_work	0.2707	20104	-
obs	0.2721	21164	88.42 %

Solvent computation

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

Displacement parameters

B_iso max: 269.5 Å² / B_iso mean: 119.4062 Å² / B_iso min: 60.94 Å²

Refinement step

Cycle: final / Resolution: 3.46→84.36 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6438	0	0	0	6438
Num. residues	-	-	-	-	887

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6559
X-RAY DIFFRACTION	f_angle_d	0.704	8932
X-RAY DIFFRACTION	f_chiral_restr	0.041	1091
X-RAY DIFFRACTION	f_plane_restr	0.006	1117
X-RAY DIFFRACTION	f_dihedral_angle_d	9.563	3824

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
3.46-3.6175	0.3857	102	0.3666	1875	67
3.6175-3.8082	0.3649	115	0.3346	2103	76
3.8082-4.0468	0.3613	141	0.2989	2424	87
4.0468-4.3592	0.293	121	0.2703	2641	93
4.3592-4.7979	0.2994	145	0.2443	2701	95
4.7979-5.492	0.2679	127	0.243	2764	97
5.492-6.9189	0.3115	147	0.286	2799	97
6.9189-84.36	0.2539	162	0.2454	2797	94

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	5.5174	-1.0748	0.9376	5.9964	-4.5385	9.8695	-0.0961	-0.5792	-0.9784	0.5891	0.6411	1.0317	-1.5762	-1.4909	-0.4795	0.8848	-0.0522	-0.1744	0.8365	0.1992	1.6112	-20.979	-10.5	-31.623
2	4.4689	-1.9287	-1.0967	1.0588	-1.3075	6.1904	0.2407	-0.4589	-0.7099	0.3713	-0.3479	0.1498	0.2259	0.0943	0.0881	0.9753	-0.0138	-0.4227	0.5852	-0.0446	1.1081	-8.972	-14.177	-29.122
3	2.5218	0.1554	-1.4796	1.6847	-3.0019	5.9424	0.4039	-0.5341	-1.4953	1.329	-0.6258	1.6726	1.7417	-0.44	0.3106	1.7163	-0.1952	-0.6146	0.719	-0.1104	0.9682	-16.762	-22.973	-24.732
4	7.5667	2.0948	0.1679	8.0127	0.4282	4.7143	-0.149	-0.1571	-0.1448	0.9324	-1.1059	0.2538	1.0163	0.4851	0.349	1.1836	0.0352	-0.0709	1.064	-0.1459	0.5876	-6.913	-14.852	-17.827
5	7.9948	1.5522	1.193	1.2188	2.0999	5.9129	-0.4119	-0.2625	-0.0525	1.0484	0.0976	-0.2075	-0.0725	0.6676	0.3792	0.7482	0.1357	-0.4494	0.9282	-0.1236	1.2352	-41.231	-52.878	-34.736
6	5.2788	-3.2388	-1.2594	5.745	3.2676	4.7106	-0.232	-0.0542	0.2235	0.599	0.1924	-0.1548	-0.0341	0.1642	-0.0839	1.1194	-0.0907	-0.5308	0.7096	0.1104	1.1214	-48.013	-52.75	-27.145
7	2.2648	-0.9557	0.2924	0.39	-0.1116	2.4473	-0.452	-0.4249	0.6028	0.4386	-1.1681	0.0348	-1.7321	-0.0291	0.6962	0.9565	0.3374	-1.456	0.7046	0.3437	1.6413	-47.393	-50.131	-19.848
8	1.7035	-0.3218	0.0569	3.5109	-1.9219	3.4113	0.6729	0.3894	1.0056	0.047	0.6482	0.3647	-1.2817	-0.7299	-0.2287	0.9977	0.2757	-1.8921	0.8111	0.4633	-0.4461	-13.21	-7.973	-66.045
9	0.5219	-1.5494	1.2354	4.5345	-3.5837	2.8157	-0.6409	-0.1009	-1.8495	-0.4182	-0.261	-1.9035	1.9475	0.7616	0.816	2.6425	-0.1917	-0.4004	1.0514	0.0203	2.7081	-6.236	-33.776	-54.704
10	7.2484	-0.8934	1.0488	1.9295	-0.7515	6.7351	-0.6435	0.3823	0.7392	0.0613	-0.194	-0.0449	-0.0266	-0.2266	0.4042	0.9459	-0.026	-0.6743	0.5691	-0.0065	1.2419	-14.289	-11.86	-58.882
11	9.5854	2.6377	-0.2803	9.7853	-8.9391	8.6887	0.3241	1.838	-2.1832	-0.7447	-1.0999	-2.3446	1.352	1.4501	0.067	1.3661	0.4674	-0.9469	1.102	-0.399	1.6542	-17.293	-31.366	-56.396
12	1.9647	-0.1326	0.5384	0.6674	0.6967	1.8172	0.6401	0.0647	0.7006	-0.0762	0.2693	-0.5278	-0.4615	-0.4176	-0.0336	0.1801	-0.514	-1.6273	0.3162	-0.7393	2.2779	-15.884	-12.134	-46.544
13	7.3818	4.0836	0.8042	2.2483	0.4681	0.0748	-0.3835	0.5913	-1.2185	-0.5782	0.2607	1.4007	1.0616	-0.6184	0.0725	1.2625	-0.3365	-0.4511	0.8296	-0.4952	2.672	-22.494	-24.627	-61.865
14	2.0437	1.8552	2.8269	1.0595	-1.2045	4.8284	-0.1547	-0.4269	0.6814	0.1407	0.8362	-0.1895	-0.8706	-0.3328	-0.1294	0.2229	-0.0707	-0.5449	0.7256	-0.1975	2.1532	-25.881	-7.779	-47.257
15	6.7232	1.9331	-1.1412	0.6498	-1.1636	7.7573	-0.0255	0.699	0.0683	-0.4183	-0.2547	0.1122	-0.1759	-0.3446	0.2399	0.7985	-0.0933	-0.1751	0.723	-0.0841	0.4703	-44.05	-56.892	-64.379
16	5.9124	2.5744	-1.3974	2.4617	-2.8029	4.054	-0.219	0.2078	-0.7543	0.3144	-0.0027	0.2326	-0.6109	-0.359	0.122	1.2343	0.0831	-0.2958	0.5218	0.0775	1.2965	-50.545	-48.072	-53.136
17	5.6758	3.4328	-1.2741	2.1127	-0.428	4.3158	-0.4097	-0.3088	-1.5471	0.3386	0.5048	0.4059	0.7067	0.7905	0.2081	1.0867	0.3114	-0.1064	0.879	0.0745	1.5276	-37.88	-56.669	-61.73
18	1.5533	0.2029	-0.0445	0.0204	-0.0147	-0.0149	-0.2856	1.7513	1.9236	-0.8868	0.2382	0.8474	-1.0866	-0.4109	-0.0904	0.3985	-0.8741	0.0829	0.758	0.1836	2.9365	-45.554	-34.193	-63.339
19	7.3872	2.8432	4.3544	1.0881	1.6655	2.5317	0.281	0.3763	0.2212	-0.4738	0.151	0.0784	-0.2145	0.9134	-0.4523	1.7714	-0.2069	-0.2925	0.6945	-0.0373	0.9796	-37.243	-37.032	-53.361
20	6.3971	2.4186	-0.9985	1.3835	0.113	3.2407	-0.2761	-0.0455	-1.3895	-0.4394	-0.3636	-0.3889	0.1812	-0.0315	0.2004	0.7235	-0.1513	-0.3144	0.6861	-0.1036	1.52	-40.823	-54.199	-46.856
21	6.3105	3.7532	-3.8448	2.2308	-2.2888	2.3404	-1.0384	2.1871	0.9315	-1.7929	1.0858	-0.2239	-1.1205	0.0348	-0.0341	1.6458	-0.3519	-0.76	0.7989	-0.1319	1.7074	-37.499	-45.518	-61.398
22	2.1781	2.0604	-1.7673	7.7927	-2.537	4.8407	-0.1738	-0.4525	0.4502	-1.1806	-0.0343	-0.8022	0.8233	0.3536	0.1372	1.4857	-0.0948	-0.5348	0.6809	-0.1452	2.7528	-30.971	-52.895	-51.124

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 2:34 )	A	2 - 34
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 38:180 )	A	38 - 180
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 181:197 )	A	181 - 197
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 198:221 )	A	198 - 221
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 4:62 )	B	4 - 62
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 63:180 )	B	63 - 180
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 181:221 )	B	181 - 221
8	X-RAY DIFFRACTION	8	( CHAIN C AND RESID 3:31 )	C	3 - 31
9	X-RAY DIFFRACTION	9	( CHAIN C AND RESID 32:39 )	C	32 - 39
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 40:109 )	C	40 - 109
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 110:126 )	C	110 - 126
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 127:184 )	C	127 - 184
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 185:202 )	C	185 - 202
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 203:226 )	C	203 - 226
15	X-RAY DIFFRACTION	15	( CHAIN D AND RESID 0:34 )	D	0 - 34
16	X-RAY DIFFRACTION	16	( CHAIN D AND RESID 37:63 )	D	37 - 63
17	X-RAY DIFFRACTION	17	( CHAIN D AND RESID 64:107 )	D	64 - 107
18	X-RAY DIFFRACTION	18	( CHAIN D AND RESID 108:117 )	D	108 - 117
19	X-RAY DIFFRACTION	19	( CHAIN D AND RESID 118:124 )	D	118 - 124
20	X-RAY DIFFRACTION	20	( CHAIN D AND RESID 125:184 )	D	125 - 184
21	X-RAY DIFFRACTION	21	( CHAIN D AND RESID 185:192 )	D	185 - 192
22	X-RAY DIFFRACTION	22	( CHAIN D AND RESID 193:224 )	D	193 - 224

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