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- PDB-5ve9: Structure of hACF7 EF1-EF2-GAR domains -

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Basic information

Entry
Database: PDB / ID: 5ve9
TitleStructure of hACF7 EF1-EF2-GAR domains
Components(Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5) x 2
KeywordsPROTEIN BINDING / Spectraplakin / EF-Hand / microtubule binding / GAS2
Function / homology
Function and homology information


regulation of neuron projection arborization / microtubule minus-end binding / regulation of epithelial cell migration / intermediate filament cytoskeleton organization / Golgi to plasma membrane protein transport / regulation of microtubule-based process / regulation of focal adhesion assembly / positive regulation of Wnt signaling pathway / positive regulation of axon extension / regulation of cell migration ...regulation of neuron projection arborization / microtubule minus-end binding / regulation of epithelial cell migration / intermediate filament cytoskeleton organization / Golgi to plasma membrane protein transport / regulation of microtubule-based process / regulation of focal adhesion assembly / positive regulation of Wnt signaling pathway / positive regulation of axon extension / regulation of cell migration / wound healing / Wnt signaling pathway / ruffle membrane / actin filament binding / actin cytoskeleton / actin binding / microtubule / cytoskeleton / cadherin binding / calcium ion binding / structural molecule activity / Golgi apparatus / RNA binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Transcriptional regulator DELLA protein N terminal / GAR domain / GAR domain superfamily / Growth-Arrest-Specific Protein 2 Domain / GAR domain profile. / Growth-Arrest-Specific Protein 2 Domain / : / Spectrin-like repeat / Spectrin repeat / Spectrin-like repeat ...Transcriptional regulator DELLA protein N terminal / GAR domain / GAR domain superfamily / Growth-Arrest-Specific Protein 2 Domain / GAR domain profile. / Growth-Arrest-Specific Protein 2 Domain / : / Spectrin-like repeat / Spectrin repeat / Spectrin-like repeat / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat / Plakin repeat superfamily / Desmoplakin, SH3 domain / SH3 domain / Plectin repeat / Plakin / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Microtubule-actin cross-linking factor 1, isoforms 1/2/3/4/5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.795 Å
AuthorsLane, T.R. / Slep, K.C.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R03HD084980 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM094415 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008570 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R37AR27883 United States
CitationJournal: Structure / Year: 2017
Title: Structure of the ACF7 EF-Hand-GAR Module and Delineation of Microtubule Binding Determinants.
Authors: Lane, T.R. / Fuchs, E. / Slep, K.C.
History
DepositionApr 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Nov 8, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5
C: Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5
B: Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4559
Polymers30,1633
Non-polymers2916
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-100 kcal/mol
Surface area13840 Å2
Unit cell
Length a, b, c (Å)92.984, 92.984, 90.446
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5 / 620 kDa actin-binding protein / ABP620 / Actin cross-linking family protein 7 / Macrophin-1 / ...620 kDa actin-binding protein / ABP620 / Actin cross-linking family protein 7 / Macrophin-1 / Trabeculin-alpha / ACF7


Mass: 10788.280 Da / Num. of mol.: 2 / Fragment: EF1-EF2 domains (UNP residues 7024-7108)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MACF1, ABP620, ACF7, KIAA0465, KIAA1251 / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9UPN3
#2: Protein Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5 / 620 kDa actin-binding protein / ABP620 / Actin cross-linking family protein 7 / Macrophin-1 / ...620 kDa actin-binding protein / ABP620 / Actin cross-linking family protein 7 / Macrophin-1 / Trabeculin-alpha / ACF7


Mass: 8586.892 Da / Num. of mol.: 1 / Fragment: GAR domain (UNP residues 7118-7191)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MACF1, ABP620, ACF7, KIAA0465, KIAA1251 / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9UPN3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsChain C is not an independent entity, but has been modeled as a separate chain because there is ...Chain C is not an independent entity, but has been modeled as a separate chain because there is insufficient electron density to determine whether it is contiguous with chain A or chain B.

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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: 3.75 Å3/Da / Density % sol: 67.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: potassium chloride, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.28295 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 24, 2016
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28295 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 11525 / % possible obs: 100 % / Redundancy: 21.2 % / Biso Wilson estimate: 69.34 Å2 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.029 / Rrim(I) all: 0.134 / Χ2: 0.988 / Net I/σ(I): 6.9 / Num. measured all: 244650
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.918.71.15611310.8620.2671.1880.81499.9
2.9-3.0220.80.95511320.930.2130.9790.863100
3.02-3.1521.60.64211380.9660.1410.6570.945100
3.15-3.3222.10.39311480.9870.0850.4031.087100
3.32-3.53220.26711210.9920.0580.2731.113100
3.53-3.821.90.19611530.9960.0430.21.107100
3.8-4.1821.80.14211470.9980.0310.1451.097100
4.18-4.7921.50.10211580.9980.0230.1050.9100
4.79-6.0321.30.09911740.9980.0220.1020.928100
6.03-5020.10.06812440.9990.0160.070.98999.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: SAD / Resolution: 2.795→41.349 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 34.69 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2788 1138 10.08 %Random selection
Rwork0.2556 10147 --
obs0.258 11285 97.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 215.41 Å2 / Biso mean: 92.7363 Å2 / Biso min: 45.65 Å2
Refinement stepCycle: final / Resolution: 2.795→41.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 1 11 2113
Biso mean--105.34 65.71 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032148
X-RAY DIFFRACTIONf_angle_d0.752877
X-RAY DIFFRACTIONf_chiral_restr0.031288
X-RAY DIFFRACTIONf_plane_restr0.002375
X-RAY DIFFRACTIONf_dihedral_angle_d12.824812
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7949-2.92210.41731360.36441158129491
2.9221-3.07610.35461330.31631219135295
3.0761-3.26870.35471420.29361227136997
3.2687-3.5210.29141430.26681270141399
3.521-3.87510.33011420.24771280142299
3.8751-4.43520.24251370.22613121449100
4.4352-5.58580.24281470.23613111458100
5.5858-41.35360.25651580.253413701528100
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)
17.5563-1.61881.61157.305-1.25748.1497-0.00440.4111.55870.2649-0.0722-1.0687-1.7395-0.24170.07980.73230.16490.18680.43690.09481.09749.78265.596110.2986
22.10244.95821.52653.8894.20476.3324-0.19752.8172-0.1657-0.1691-0.0606-1.0135-0.34330.52630.31280.64850.19760.06370.67770.28220.830647.49142.46980.3165
38.0987-1.12670.54664.67482.26123.94860.6260.46770.0374-0.2366-0.83371.1683-0.3798-0.20130.11980.68920.1769-0.00740.4184-0.00720.838842.9642-1.41748.1747
48.03142.86084.04149.55385.22787.15330.1099-0.9046-0.27540.9898-0.30291.36570.2605-0.71240.150.62770.02340.12680.61790.14740.854336.8451-24.884225.9358
58.10996.57951.05228.78291.84647.86080.1479-1.1041-1.1784-0.3743-0.4426-21.7820.66470.40480.75990.13130.15540.56180.12550.71346.7386-25.773724.9573
67.04354.0751-1.79397.9743-7.21739.0135-0.3380.6375-0.6552-0.41450.1272-0.39020.5392-0.56470.19750.6050.00680.11720.4101-0.00460.65141.7893-26.144215.3313
74.91492.3494-4.36531.1656-2.21978.75571.14740.06060.8050.1511-0.0225-0.3696-0.0660.2146-1.02420.61070.1596-0.08030.63290.22411.107649.9046-9.18414.6654
82.01060.02352.01827.48632.46492.14451.19232.9033-0.1433-1.8337-0.5657-1.55780.25841.3806-0.90561.06840.23570.24910.8611-0.04611.001267.54-15.8535.6608
98.5061-0.7809-3.88238.4876-0.23637.4152-0.71080.53720.04510.5535-0.3412-2.02480.38532.03980.640.59920.1093-0.16310.82780.10821.384775.5782-19.529915.7092
106.91261.3415-3.13685.4971-5.58256.33090.5242-0.61820.60841.272-0.0661-0.7294-0.95870.9579-0.28310.8340.1021-0.11340.5242-0.22331.190969.2332-14.317722.7983
115.9188-0.5311-0.29523.0604-3.05173.40110.5966-0.4752.2566-0.1966-0.743-1.2736-0.43420.68310.12890.66080.1266-0.05280.42490.09861.226562.3276-9.378613.7806
129.5602-3.12321.1752.5179-0.04615.89120.84010.3882-0.1381-0.5779-0.4635-0.21620.0845-0.0936-0.2790.72470.1214-0.10650.4858-0.09981.102362.2233-22.645418.8312
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7019 through 7051 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 7052 through 7076 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 7077 through 7106 )A0
4X-RAY DIFFRACTION4chain 'C' and (resid 7116 through 7145 )C0
5X-RAY DIFFRACTION5chain 'C' and (resid 7146 through 7160 )C0
6X-RAY DIFFRACTION6chain 'C' and (resid 7161 through 7189 )C0
7X-RAY DIFFRACTION7chain 'B' and (resid 7016 through 7025 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 7026 through 7040 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 7041 through 7051 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 7052 through 7071 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 7072 through 7087 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 7088 through 7106 )B0

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