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- PDB-9ijx: Crystal structure of the mouse Spef1 coiled-coil domain -

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Basic information

Entry
Database: PDB / ID: 9ijx
TitleCrystal structure of the mouse Spef1 coiled-coil domain
ComponentsSperm flagellar protein 1
KeywordsCYTOSOLIC PROTEIN / component of motile cilia axoneme
Function / homology
Function and homology information


axonemal central apparatus / axonemal central apparatus assembly / regulation of Wnt signaling pathway, planar cell polarity pathway / 9+2 motile cilium / cilium movement / ciliary tip / negative regulation of microtubule depolymerization / filopodium assembly / microtubule bundle formation / lamellipodium assembly ...axonemal central apparatus / axonemal central apparatus assembly / regulation of Wnt signaling pathway, planar cell polarity pathway / 9+2 motile cilium / cilium movement / ciliary tip / negative regulation of microtubule depolymerization / filopodium assembly / microtubule bundle formation / lamellipodium assembly / motile cilium / microvillus / axoneme / stress fiber / filopodium / cell migration / lamellipodium / actin binding / basolateral plasma membrane / microtubule binding / microtubule / apical plasma membrane / cytoplasm
Similarity search - Function
: / CH-like domain in sperm protein / CH-like domain in sperm protein / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile.
Similarity search - Domain/homology
Sperm flagellar protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsRen, J. / Li, D. / Feng, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971160 China
CitationJournal: To Be Published
Title: Coiled-coil of Sperm flagellar protein 1
Authors: Ren, J. / Li, D. / Feng, W.
History
DepositionJun 25, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sperm flagellar protein 1
B: Sperm flagellar protein 1
C: Sperm flagellar protein 1
D: Sperm flagellar protein 1
E: Sperm flagellar protein 1
F: Sperm flagellar protein 1


Theoretical massNumber of molelcules
Total (without water)48,0616
Polymers48,0616
Non-polymers00
Water00
1
A: Sperm flagellar protein 1
B: Sperm flagellar protein 1


Theoretical massNumber of molelcules
Total (without water)16,0202
Polymers16,0202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-29 kcal/mol
Surface area7710 Å2
MethodPISA
2
C: Sperm flagellar protein 1
D: Sperm flagellar protein 1


Theoretical massNumber of molelcules
Total (without water)16,0202
Polymers16,0202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-25 kcal/mol
Surface area7740 Å2
MethodPISA
3
E: Sperm flagellar protein 1
F: Sperm flagellar protein 1


Theoretical massNumber of molelcules
Total (without water)16,0202
Polymers16,0202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-24 kcal/mol
Surface area7480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.150, 104.360, 72.270
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
1313
1414
1515

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Sperm flagellar protein 1 / Calponin-homology and microtubule-associated protein


Mass: 8010.150 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Spef1, Clamp / Plasmid: pET32a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q99JL1
Has protein modificationN

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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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M BICINE, 3%(w/v) Dextran sulfate sodium, 15% (w/v) PEG20000.
PH range: 7.5-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.949 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 15881 / % possible obs: 96.6 % / Redundancy: 4.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.049 / Net I/σ(I): 11.4
Reflection shellResolution: 2.45→2.51 Å / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1167 / CC1/2: 0.609 / Rpim(I) all: 0.415 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→26.09 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 17.023 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23436 789 5 %RANDOM
Rwork0.19535 ---
obs0.19707 15061 95.88 %-
Solvent computationIon probe radii: 1.2 Å / Shrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å20.08 Å2
2--40.48 Å20 Å2
3----38.97 Å2
Refinement stepCycle: 1 / Resolution: 2.45→26.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2445 0 0 0 2445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132451
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172476
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.6363278
X-RAY DIFFRACTIONr_angle_other_deg1.1331.5855749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3015292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.19623.137153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.59215547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9831524
X-RAY DIFFRACTIONr_chiral_restr0.0490.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022632
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02436
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5368.0521186
X-RAY DIFFRACTIONr_mcbond_other1.5378.0531185
X-RAY DIFFRACTIONr_mcangle_it2.62112.0661472
X-RAY DIFFRACTIONr_mcangle_other2.6212.0651473
X-RAY DIFFRACTIONr_scbond_it1.4068.2541265
X-RAY DIFFRACTIONr_scbond_other1.4068.2551266
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.512.3111807
X-RAY DIFFRACTIONr_long_range_B_refined4.92795.6342714
X-RAY DIFFRACTIONr_long_range_B_other4.92695.6212715
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A12920.17
12B12920.17
21A14770.14
22C14770.14
31A12590.16
32D12590.16
41A14800.13
42E14800.13
51A11900.16
52F11900.16
61B13550.17
62C13550.17
71B13530.16
72D13530.16
81B13570.17
82E13570.17
91B12320.15
92F12320.15
101C13230.16
102D13230.16
111C15400.14
112E15400.14
121C12060.16
122F12060.16
131D13290.16
132E13290.16
141D12180.15
142F12180.15
151E12030.14
152F12030.14
LS refinement shellResolution: 2.45→2.51 Å
Num. reflection% reflection
Rfree63 -
Rwork1035 -
obs-89.05 %
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)
11.1531-1.28592.78073.35-7.148315.53130.03240.01960.1364-0.1661-0.1779-0.01050.3230.30230.14550.19610.0095-0.01080.042-0.01280.169122.4760.43413.894
21.16310.3025-1.1111.4387-4.031416.06360.04330.02350.0303-0.13470.0256-0.04470.182-0.2655-0.06890.1675-0.0059-0.00250.0179-0.02770.167217.80253.0716.223
33.82090.1939-7.01880.3945-0.953815.2437-0.1294-0.1068-0.1827-0.0078-0.08960.04470.06660.08470.21890.1317-0.01930.01150.09610.01190.17116.90132.53732.567
41.64760.0863-2.18541.7196-2.212115.2550.1592-0.21640.0190.01530.01910.1767-0.00470.0507-0.17840.1056-0.0474-0.02440.0573-0.00960.16510.33940.1631.121
51.81791.64084.76182.47975.688515.3096-0.1636-0.09190.0253-0.053-0.1210.1582-0.0639-0.24330.28460.1214-0.0193-0.02070.0738-0.00340.127114.1919.386-9.345
61.0422-0.12992.66620.44550.40399.5329-0.09590.07410.0271-0.0337-0.00360.05170.01330.14020.09960.0977-0.0273-0.00640.05770.0050.089522.3718.682-9.295
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A176 - 227
2X-RAY DIFFRACTION2B182 - 229
3X-RAY DIFFRACTION3C177 - 230
4X-RAY DIFFRACTION4D183 - 229
5X-RAY DIFFRACTION5E176 - 229
6X-RAY DIFFRACTION6F183 - 225

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