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- PDB-7lr3: Complex of Fab 2/6.14 with domain 3 of P. berghei HAP2 -

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Basic information

Entry
Database: PDB / ID: 7lr3
TitleComplex of Fab 2/6.14 with domain 3 of P. berghei HAP2
Components
  • (D3_2/6.14 Fab ...) x 2
  • (Hapless 2) x 2
KeywordsSURFACTANT PROTEIN/IMMUNE SYSTEM / transmission-blocking malaria vaccine / membrane fusion / gamete fusogen / monoclonal antibody / SURFACTANT PROTEIN / SURFACTANT PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


fusion of sperm to egg plasma membrane involved in single fertilization / fertilization / lipid binding / plasma membrane
Similarity search - Function
HAP2/GCS1 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Hapless 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Plasmodium berghei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFeng, J. / Dong, X.C. / Lu, C.F. / Springer, T.A.
CitationJournal: Elife / Year: 2021
Title: Structural basis of malaria transmission blockade by a monoclonal antibody to gamete fusogen HAP2.
Authors: Feng, J. / Dong, X. / DeCosta, A. / Su, Y. / Angrisano, F. / Sala, K.A. / Blagborough, A.M. / Lu, C. / Springer, T.A.
History
DepositionFeb 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 19, 2022Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: D3_2/6.14 Fab light chain
H: D3_2/6.14 Fab heavy chain
D: Hapless 2
C: Hapless 2
A: D3_2/6.14 Fab heavy chain
B: D3_2/6.14 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,4558
Polymers124,1106
Non-polymers3442
Water32418
1
L: D3_2/6.14 Fab light chain
H: D3_2/6.14 Fab heavy chain
D: Hapless 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4165
Polymers62,0713
Non-polymers3442
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Hapless 2
A: D3_2/6.14 Fab heavy chain
B: D3_2/6.14 Fab light chain


Theoretical massNumber of molelcules
Total (without water)62,0393
Polymers62,0393
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.250, 122.580, 168.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number16
Space group name H-MP222

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Components

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Protein , 2 types, 2 molecules DC

#3: Protein Hapless 2 / Generative cell specific-1


Mass: 13897.661 Da / Num. of mol.: 1 / Mutation: N516T, S533N, N539Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium berghei (eukaryote) / Gene: HAP2, GCS1, PB000710.01.0 / Production host: Homo sapiens (human) / References: UniProt: Q4YCF6
#4: Protein Hapless 2 / Generative cell specific-1


Mass: 13865.662 Da / Num. of mol.: 1 / Mutation: N516T, S533N, N539Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium berghei (eukaryote) / Gene: HAP2, GCS1, PB000710.01.0 / Production host: Homo sapiens (human) / References: UniProt: Q4YCF6

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Antibody , 2 types, 4 molecules LBHA

#1: Antibody D3_2/6.14 Fab light chain


Mass: 23633.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody D3_2/6.14 Fab heavy chain


Mass: 24540.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 20 molecules

#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.26 Å3/Da / Density % sol: 62.23 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 10 mM HEPES, 20 mM Proline

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 40463 / % possible obs: 99.3 % / Redundancy: 3.8 % / CC1/2: 0.997 / Net I/av σ(I): 8.42 / Net I/σ(I): 12.8
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 0.52 / Num. unique obs: 4935 / CC1/2: 0.109 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XSCALEdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A6D

2a6d


Resolution: 2.8→42.767 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.09
RfactorNum. reflection% reflection
Rfree0.2918 1263 3.14 %
Rwork0.2529 --
obs0.2541 40262 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→42.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7945 0 22 18 7985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310586
X-RAY DIFFRACTIONf_angle_d0.54814375
X-RAY DIFFRACTIONf_dihedral_angle_d11.66303
X-RAY DIFFRACTIONf_chiral_restr0.0451607
X-RAY DIFFRACTIONf_plane_restr0.0061811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.91210.45141370.36514223X-RAY DIFFRACTION98
2.9121-3.04460.40771380.33654241X-RAY DIFFRACTION99
3.0446-3.20510.36261370.30354261X-RAY DIFFRACTION99
3.2051-3.40580.31331390.27934289X-RAY DIFFRACTION99
3.4058-3.66860.29371400.25734310X-RAY DIFFRACTION99
3.6686-4.03750.32171400.24954340X-RAY DIFFRACTION99
4.0375-4.62120.26311420.22584366X-RAY DIFFRACTION99
4.6212-5.81990.24991420.22974407X-RAY DIFFRACTION99
5.8199-42.7670.28421480.25044562X-RAY DIFFRACTION98
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)
15.75610.8464-1.18247.7426-1.03532.9026-0.1473-0.6474-0.21290.46790.3623-0.3953-0.05640.0215-0.15990.3310.0833-0.04781.0928-0.39950.575510.71728.11133.7464
21.981.6682-1.43098.67031.43247.8985-0.1535-0.97610.13210.57590.3634-0.1833-0.1062-0.694-0.20780.47010.1123-0.12081.0393-0.18040.42110.62926.138437.024
38.1868-0.91290.23320.1878-0.34091.31470.1320.0066-1.8221-0.0161-0.02810.35190.36560.2435-0.21430.6032-0.0042-0.05651.8231-1.1322.4952-12.68425.836157.7618
42.5637-3.42120.42754.5853-0.67795.30320.2122-0.21160.7515-0.27530.0716-0.3256-0.78220.1841-0.22750.6126-0.06710.18290.5327-0.16271.07897.951826.989921.9612
58.171-2.4716-0.30351.2743-0.21164.05230.18980.18820.5887-0.3116-0.1018-0.4604-0.5109-0.1251-0.0430.4656-0.00820.13570.6684-0.38521.20587.313723.899623.9905
68.04610.38172.36181.893-0.65511.2260.3810.10130.45270.1588-0.50180.3279-0.10970.27630.0730.60620.03690.01082.1981-1.21461.8468-3.203636.634751.0068
71.8008-3.0939-2.17685.69262.69265.5985-0.57560.0427-2.04770.5920.3111-0.15550.84880.52780.25240.72990.1482-0.12731.0071-0.51932.126726.73930.552967.5744
82.1093-0.8218-1.32490.61780.55831.3401-0.0570.2251-0.56590.1224-0.1010.33510.31360.364-0.00190.74490.3302-0.04291.9081-1.62992.94749.717514.686342.8003
92.546-1.7718-1.3082.11960.6582.00160.07380.9669-0.4286-0.34490.0757-0.6242-0.26930.1661-0.22060.51960.14330.05371.5999-0.74091.169929.009847.208353.2347
102.3833-0.796-0.23420.6736-0.17720.49460.37060.7385-0.7078-0.3248-0.06480.5390.294-0.00430.1420.42140.3214-0.31462.2304-1.57082.713439.292825.269235.2958
112.07662.6657-0.50649.3734-0.85989.03830.64510.09840.4913-0.1274-0.3457-0.5318-1.02611.3322-0.2820.58320.08710.10410.8428-0.12240.679817.547462.076972.4451
126.1922-2.506-4.02837.6587-2.22714.87510.82771.0717-0.0237-1.1251-0.2972-0.3183-0.16990.9556-0.51060.73540.07260.11761.1337-0.34720.81523.77512.80034.8206
138.9046-4.4777-2.88878.1968-0.94771.90840.97671.64540.1137-1.4496-0.0798-0.39420.08640.9275-0.86870.93950.25740.13121.0846-0.43441.099123.07488.58298.1084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain B and resseq 1:106 and altloc A
2X-RAY DIFFRACTION2chain B and resseq 1:106 and altloc B
3X-RAY DIFFRACTION3chain B and resseq 107:211
4X-RAY DIFFRACTION4chain A and resseq 1:119 and altloc A
5X-RAY DIFFRACTION5chain A and resseq 1:119 and altloc B
6X-RAY DIFFRACTION6chain A and resseq 120:219
7X-RAY DIFFRACTION7chain L and resseq 1:106
8X-RAY DIFFRACTION8chain L and resseq 107:210
9X-RAY DIFFRACTION9chain H and resseq 1:119
10X-RAY DIFFRACTION10chain H and resseq 120:216
11X-RAY DIFFRACTION11chain D
12X-RAY DIFFRACTION12chain C and altloc A
13X-RAY DIFFRACTION13chain C and altloc B

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