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- PDB-8yhz: The co-crystal structure of the Fab fragment of Ab-1080 with NaV1... -

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Basic information

Entry
Database: PDB / ID: 8yhz
TitleThe co-crystal structure of the Fab fragment of Ab-1080 with NaV1.7 VSDII peptide
Components
  • Heavy chain of 1080 Fab
  • Light chain of 1080 Fab
  • Sodium channel protein type 9 subunit alpha
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / inhibitor / NaV1.7 / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


action potential propagation / detection of mechanical stimulus involved in sensory perception / cardiac muscle cell action potential involved in contraction / node of Ranvier / voltage-gated sodium channel complex / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / Phase 0 - rapid depolarisation / behavioral response to pain / detection of temperature stimulus involved in sensory perception of pain ...action potential propagation / detection of mechanical stimulus involved in sensory perception / cardiac muscle cell action potential involved in contraction / node of Ranvier / voltage-gated sodium channel complex / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / Phase 0 - rapid depolarisation / behavioral response to pain / detection of temperature stimulus involved in sensory perception of pain / neuronal action potential / axon terminus / sensory perception of pain / sodium ion transmembrane transport / post-embryonic development / response to toxic substance / circadian rhythm / Sensory perception of sweet, bitter, and umami (glutamate) taste / inflammatory response / axon / plasma membrane
Similarity search - Function
Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / SCN5A-like, C-terminal IQ motif / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site ...Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / SCN5A-like, C-terminal IQ motif / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Sodium channel protein type 9 subunit alpha
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsDu, J. / Zhang, Y. / Zhu, R. / Ding, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82373774 China
CitationJournal: Cell Rep Med / Year: 2024
Title: Intra-channel bi-epitopic crosslinking unleashes ultrapotent antibodies targeting Na V 1.7 for pain alleviation.
Authors: Zhang, Y. / Ding, Y. / Zeng, Z. / Zhu, R. / Zheng, P. / Fan, S. / Cao, Q. / Chen, H. / Ren, W. / Wu, M. / Wang, L. / Du, J.
History
DepositionFeb 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.page_first ..._audit_author.name / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 4, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Light chain of 1080 Fab
H: Heavy chain of 1080 Fab
P: Sodium channel protein type 9 subunit alpha


Theoretical massNumber of molelcules
Total (without water)47,4143
Polymers47,4143
Non-polymers00
Water9,134507
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-26 kcal/mol
Surface area19300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.965, 78.965, 147.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Antibody Light chain of 1080 Fab


Mass: 23444.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#2: Antibody Heavy chain of 1080 Fab


Mass: 22567.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#3: Protein/peptide Sodium channel protein type 9 subunit alpha / NaV1.7 VSDII peptide / Neuroendocrine sodium channel / hNE-Na / Peripheral sodium channel 1 / PN1 / ...NaV1.7 VSDII peptide / Neuroendocrine sodium channel / hNE-Na / Peripheral sodium channel 1 / PN1 / Sodium channel protein type IX subunit alpha / Voltage-gated sodium channel subunit alpha Nav1.7


Mass: 1401.521 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15858
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M potassium thiocyanate, 25% W/V Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.62→28.67 Å / Num. obs: 59782 / % possible obs: 99.92 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 29.4
Reflection shellResolution: 1.62→1.678 Å / Rmerge(I) obs: 0.107 / Num. unique obs: 59782

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→28.65 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 2000 3.39 %RANDOM
Rwork0.1937 ---
obs0.1942 58921 98.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.62→28.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 0 507 3816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d1.026
X-RAY DIFFRACTIONf_dihedral_angle_d14.8481191
X-RAY DIFFRACTIONf_chiral_restr0.063534
X-RAY DIFFRACTIONf_plane_restr0.007584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.660.30911300.29843710X-RAY DIFFRACTION92
1.66-1.70.27981350.27733847X-RAY DIFFRACTION95
1.7-1.750.27991390.2533930X-RAY DIFFRACTION96
1.75-1.810.28041390.2343966X-RAY DIFFRACTION97
1.81-1.880.22931410.22514019X-RAY DIFFRACTION99
1.88-1.950.25391430.22174038X-RAY DIFFRACTION99
1.95-2.040.25021420.22754064X-RAY DIFFRACTION99
2.04-2.150.21341450.20674116X-RAY DIFFRACTION100
2.15-2.280.21151430.20654084X-RAY DIFFRACTION100
2.28-2.460.23961460.21264139X-RAY DIFFRACTION100
2.46-2.70.25561450.22064142X-RAY DIFFRACTION100
2.7-3.10.2331470.21054189X-RAY DIFFRACTION100
3.1-3.90.20441490.17534234X-RAY DIFFRACTION100
3.9-28.650.16021560.16094443X-RAY DIFFRACTION100
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)
11.26060.3951-0.15761.68-0.24371.2340.0565-0.2925-0.26990.0378-0.1208-0.26270.05450.17240.07530.26430.0149-0.00630.29330.02220.3196-3.0022-19.1995-20.5806
21.80620.05540.26081.52080.42651.474-0.04010.04640.0129-0.2670.0030.19210.06670.02020.06470.25860.0045-0.00240.2512-0.0140.2586-12.9771-20.0153-28.939
32.79573.2495-1.8595.3954-2.7272.5385-0.1911-0.1257-0.3261-0.1538-0.0895-0.26810.29960.10430.31310.28730.030.01140.26180.00360.3322-5.8957-25.4616-26.6979
42.55680.5374-0.26261.6030.19220.7673-0.10510.06090.1074-0.18220.0614-0.01260.08850.0280.01720.24090.0021-0.01460.21970.00590.2136-10.4151-17.2618-23.1342
50.3489-0.2151-0.17051.81890.2820.55280.2619-0.01510.1276-0.0407-0.2-0.3063-0.2082-0.1321-0.00810.3637-0.0268-0.00140.27830.00610.33614.822811.6547-18.3005
62.9693-1.2737-1.19613.10141.32362.28520.0786-0.36590.31270.0925-0.29960.3689-0.4402-0.23920.23080.43990.0263-0.00350.3588-0.10580.3781-6.388920.377-11.449
70.5612-0.9765-0.98582.61671.76461.7237-0.0203-0.3016-0.05770.61130.1-0.15660.3920.20430.03640.4131-0.017-0.0240.36320.01850.31525.18986.1131-11.5911
81.1784-0.2813-0.73251.89981.11.87330.0746-0.3119-0.03690.2033-0.1459-0.02430.01160.10750.10430.3705-0.0246-0.04110.38320.0370.2970.12456.2803-13.6908
91.6010.1646-0.19091.68240.50691.77710.1947-0.43440.32740.2481-0.0267-0.1651-0.0721-0.1861-0.13890.3571-0.0338-0.03790.3571-0.05910.33363.445417.8246-7.6326
100.86470.43170.08721.68310.66970.6250.02620.04210.00830.0462-0.0460.1037-0.069-0.0780.01180.2573-0.0006-0.00310.2677-0.0130.2597-28.126-9.4047-20.7041
111.5767-0.4442-1.2042.73530.55833.18080.0246-0.199-0.1457-0.17190.2491-0.9131-0.05810.9109-0.11770.3818-0.02940.07650.4739-0.14630.4859-0.858621.6531-20.097
122.90190.8131-0.18071.35230.44651.16940.10240.24650.2726-0.0705-0.05080.0122-0.21550.0316-0.00070.32220.040.01340.2840.02620.246-11.206415.0284-21.9129
130.987-2.0128-0.13064.21190.69645.59090.12860.4959-0.5045-0.4275-0.10590.77590.6449-0.86580.3570.4747-0.0683-0.030.3922-0.05960.4964-31.8076-28.1967-27.7797
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 0 through 23 )
2X-RAY DIFFRACTION2chain 'L' and (resid 24 through 61 )
3X-RAY DIFFRACTION3chain 'L' and (resid 62 through 75 )
4X-RAY DIFFRACTION4chain 'L' and (resid 76 through 111 )
5X-RAY DIFFRACTION5chain 'L' and (resid 112 through 125 )
6X-RAY DIFFRACTION6chain 'L' and (resid 126 through 141 )
7X-RAY DIFFRACTION7chain 'L' and (resid 142 through 154 )
8X-RAY DIFFRACTION8chain 'L' and (resid 155 through 178 )
9X-RAY DIFFRACTION9chain 'L' and (resid 179 through 217 )
10X-RAY DIFFRACTION10chain 'H' and (resid 1 through 118 )
11X-RAY DIFFRACTION11chain 'H' and (resid 119 through 133 )
12X-RAY DIFFRACTION12chain 'H' and (resid 134 through 214 )
13X-RAY DIFFRACTION13chain 'P' and (resid 210 through 219 )

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