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- PDB-7qqm: The PDZ domain of LRRC7 fused with ANXA2 -

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Basic information

Entry
Database: PDB / ID: 7qqm
TitleThe PDZ domain of LRRC7 fused with ANXA2
ComponentsLeucine-rich repeat-containing protein 7,Annexin A2
KeywordsPEPTIDE BINDING PROTEIN / PDZ / linear motif / crystallization chaperone
Function / homology
Function and homology information


: / AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair ...: / AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / myelin sheath adaxonal region / neurotransmitter receptor transport, endosome to postsynaptic membrane / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / cornified envelope / vesicle budding from membrane / establishment or maintenance of epithelial cell apical/basal polarity / axon initial segment / osteoclast development / plasma membrane protein complex / calcium-dependent phospholipid binding / negative regulation of receptor internalization / Dissolution of Fibrin Clot / S100 protein binding / collagen fibril organization / Assembly and cell surface presentation of NMDA receptors / vesicle membrane / : / epithelial cell apoptotic process / phosphatidylserine binding / positive regulation of receptor recycling / receptor clustering / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of exocytosis / Long-term potentiation / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / cytoskeletal protein binding / fibrinolysis / lipid droplet / phosphatidylinositol-4,5-bisphosphate binding / Ras activation upon Ca2+ influx through NMDA receptor / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / response to activity / adherens junction / lung development / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / sarcolemma / cell-cell adhesion / positive regulation of neuron projection development / RNA polymerase II transcription regulator complex / nuclear matrix / specific granule lumen / calcium-dependent protein binding / azurophil granule lumen / late endosome membrane / melanosome / RAF/MAP kinase cascade / midbody / protease binding / : / basolateral plasma membrane / angiogenesis / vesicle / early endosome / postsynaptic density / endosome / lysosomal membrane / calcium ion binding / Neutrophil degranulation / protein kinase binding / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / RNA binding / extracellular exosome / extracellular region / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Annexin A2 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin A2 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / : / Annexin V; domain 1 / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / PDZ domain / Pdz3 Domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Leucine-rich repeat / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Leucine-rich repeat domain superfamily / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Annexin A2 / Leucine-rich repeat-containing protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCousido-Siah, A. / Trave, G. / Gogl, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: A scalable strategy to solve structures of PDZ domains and their complexes.
Authors: Cousido-Siah, A. / Carneiro, L. / Kostmann, C. / Ecsedi, P. / Nyitray, L. / Trave, G. / Gogl, G.
History
DepositionJan 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine-rich repeat-containing protein 7,Annexin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2828
Polymers46,8451
Non-polymers4377
Water8,989499
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.780, 70.080, 102.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Leucine-rich repeat-containing protein 7,Annexin A2 / Densin-180 / Densin / Protein LAP1 / Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 ...Densin-180 / Densin / Protein LAP1 / Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy chain / Chromobindin-8 / Lipocortin II / Placental anticoagulant protein IV / PAP-IV / Protein I / p36


Mass: 46845.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: LRRC7, KIAA1365, LAP1, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D
Production host: Escherichia coli (E. coli) / References: UniProt: Q96NW7, UniProt: P07355
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Potassium thiocyanate 0.1 M Sodium bromide 0.1 M MES 6.5 12 % v/v PEG Smear High

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→45.481 Å / Num. obs: 57570 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 1 / Rrim(I) all: 0.106 / Net I/σ(I): 18.28
Reflection shellResolution: 1.6→1.64 Å / Mean I/σ(I) obs: 1.57 / Num. unique obs: 4207 / CC1/2: 0.572 / Rrim(I) all: 1.952

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N7D

5n7d


Resolution: 1.6→45.481 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1983 2872 5 %
Rwork0.1697 54625 -
obs0.1711 57497 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.22 Å2 / Biso mean: 28.3666 Å2 / Biso min: 13.19 Å2
Refinement stepCycle: final / Resolution: 1.6→45.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3277 0 28 499 3804
Biso mean--27.13 39.49 -
Num. residues----413
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.6-1.62620.28061360.26762574
1.6262-1.65430.28511350.25662561
1.6543-1.68440.28421340.2452555
1.6844-1.71680.26591360.23732576
1.7168-1.75180.24581350.21862561
1.7518-1.78990.26391350.21292567
1.7899-1.83150.20961350.19252572
1.8315-1.87730.21371350.19012569
1.8773-1.92810.23321360.18572578
1.9281-1.98480.20471360.17972582
1.9848-2.04890.21071370.17382603
2.0489-2.12210.17761360.16972570
2.1221-2.20710.16751360.16282582
2.2071-2.30750.18881370.16522605
2.3075-2.42920.21241360.16172604
2.4292-2.58140.20471370.16882602
2.5814-2.78070.18931380.17032607
2.7807-3.06040.18661390.15592643
3.0604-3.50310.19691370.15462639
3.5031-4.4130.16411390.13942680
4.413-45.4810.19781470.17282795
Refinement TLS params.

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

IDL11 (°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)
12.63430.95650.05443.8606-0.62672.30480.0249-0.1190.09080.27590.00680.2748-0.0815-0.0972-0.00530.17460.01230.04460.1419-0.00360.1364-31.41173.818422.565
23.4642-0.1199-0.07262.74080.1942.4320.0434-0.05890.2431-0.0713-0.02510.0909-0.3291-0.0884-0.00510.1925-0.00060.02480.11120.00820.1428-21.204620.47679.5497
31.1951.71420.32365.1970.85012.1792-0.06480.1080.0619-0.21810.1733-0.0425-0.17830.0784-0.11650.13220.0055-0.00280.15860.01620.1068-23.2834.2133-13.712
40.77310.49820.34731.03670.37590.9152-0.04770.0765-0.0822-0.02210.0499-0.01260.05950.034-0.01660.15410.00270.01730.1392-0.00320.1608-23.1976-9.8829-3.1298
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1443 through 1533 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1534 through 1621 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1622 through 1703 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1704 through 1855 )A0

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