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- PDB-8fz2: Crystal structure of Fab460 in complex with MPER peptide -

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Basic information

Entry
Database: PDB / ID: 8fz2
TitleCrystal structure of Fab460 in complex with MPER peptide
Components
  • Fab460, H chain
  • Fab460, L chain
  • Transmembrane protein gp41
KeywordsIMMUNE SYSTEM / Fab / HIV / MPER / membrane-proximal external region / vaccine
Function / homology
Function and homology information


symbiont-mediated suppression of host complement activation by recruitment of complement control protein / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...symbiont-mediated suppression of host complement activation by recruitment of complement control protein / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMus musculus (house mouse)
Human immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsTan, K. / Kim, M. / Reinherz, E.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI145509 United States
CitationJournal: Nat Commun / Year: 2023
Title: Inadequate structural constraint on Fab approach rather than paratope elicitation limits HIV-1 MPER vaccine utility.
Authors: Tan, K. / Chen, J. / Kaku, Y. / Wang, Y. / Donius, L. / Khan, R.A. / Li, X. / Richter, H. / Seaman, M.S. / Walz, T. / Hwang, W. / Reinherz, E.L. / Kim, M.
History
DepositionJan 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / pdbx_entity_src_syn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._entity.pdbx_description / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.2Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab460, L chain
H: Fab460, H chain
P: Transmembrane protein gp41


Theoretical massNumber of molelcules
Total (without water)50,3973
Polymers50,3973
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-28 kcal/mol
Surface area20100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.069, 144.069, 149.445
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Antibody Fab460, L chain


Mass: 23333.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): 293-F cells / Production host: Homo sapiens (human)
#2: Antibody Fab460, H chain


Mass: 24165.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): 293-F cells / Production host: Homo sapiens (human)
#3: Protein/peptide Transmembrane protein gp41 / TM / Glycoprotein 41 / gp41


Mass: 2897.349 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Human immunodeficiency virus type 1 group M subtype B (strain 89.6)
References: UniProt: Q73372
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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M ammonium phosphate monobasic, 0.1 M Tris-HCl 50% v/v (+/-)-2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2019
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.5→42 Å / Num. obs: 7498 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 68.19 Å2 / CC1/2: 0.966 / CC star: 0.991 / Rmerge(I) obs: 0.231 / Rpim(I) all: 0.094 / Rrim(I) all: 0.25 / Χ2: 0.941 / Net I/σ(I): 8.67
Reflection shellResolution: 3.5→3.58 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.158 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 482 / CC1/2: 0.549 / CC star: 0.842 / Rpim(I) all: 0.51 / Rrim(I) all: 1.27 / Χ2: 0.986 / % possible all: 94.1

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIX1.15.1_3469refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→41.59 Å / SU ML: 0.5945 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.0502
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3099 426 4.43 %
Rwork0.262 9184 -
obs0.2642 6949 65.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.22 Å2
Refinement stepCycle: LAST / Resolution: 3.5→41.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3010 0 0 0 3010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00153080
X-RAY DIFFRACTIONf_angle_d0.47024226
X-RAY DIFFRACTIONf_chiral_restr0.0408489
X-RAY DIFFRACTIONf_plane_restr0.0034546
X-RAY DIFFRACTIONf_dihedral_angle_d1.98311774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-4.010.4028800.32321923X-RAY DIFFRACTION41.26
4.01-5.050.27681500.26232865X-RAY DIFFRACTION62.16
5.05-41.590.31231960.24624396X-RAY DIFFRACTION94.23
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)
11.01698533320.03555272848010.3239154830171.628683118730.1684752119491.926737833680.008663741659770.429682122104-0.23551977848-0.3377488687260.4252348893120.3488374649610.342561800375-0.664800273530.3569746787810.0499607376344-0.233156078812-0.4692760476670.460272063071-0.3382109076020.421613465709-19.0802323102-5.33156249091-18.1667872506
21.1403527598-0.937116981376-1.06859828811.15061292995-0.05480036554293.69942830278-0.3476955233760.562278240555-0.341789672069-0.443002587346-0.1220114236930.5389717605050.594820738032-1.46014155994-0.2848747081140.203139040648-0.00556278918728-0.3740092088170.4540493438120.09560438059560.659078479595-21.6286679287-3.42291636232-14.9993630499
30.859954768399-0.2919861072681.504165602211.36082645121-0.03499150044922.744411924650.01907199604921.05525559831-0.381179725124-1.294531359110.275128219080.1685711285480.4713821197980.0756847759994-0.3443959535360.99006881331-0.649319247562-0.6335737687521.02767152808-0.9498338165911.05062516755-27.972752003-20.8689636668-40.6690867556
40.8548652915711.00390923906-0.1321065282976.09081003018-0.8853202323380.131232879184-0.4469837950541.43716658715-1.33777164974-1.000080160420.560024172309-1.437890994720.5770756953130.1135547349860.03881214050530.916303829827-0.6549834472350.01424487702911.83880185053-0.2284298911281.03507930017-25.7963907742-21.8236911009-39.7130197245
56.1205974033-1.95960831511-2.424305907481.057273588560.7011690735591.531574359560.927027486610.523215642014-0.313972840653-0.703761830022-0.0904354098124-1.643892486060.1170996999030.0344298462694-0.5349555720780.8133411983350.210127642468-0.008967890076941.38621972113-0.6334965855892.48964487539-17.760975451-22.7360097202-48.7940107776
64.42500886837-3.61505705772-1.105763474044.692270412130.8400513407614.563176385090.1092481394020.138218113503-0.2367930061410.1681588404670.273528898298-0.6015133191940.672308853307-0.611955788401-0.4273676646720.910411363449-0.229818819257-0.3612705712031.59578717163-0.4698733045331.06238054982-31.5741990584-16.0356324275-33.6951626828
71.379762808060.870629435149-0.01519191422622.02699222735-0.2149122437570.0287256742765-0.6533856700091.18192773222-0.597758545518-0.9875559302030.612637014589-0.9120877027260.0325385695588-0.11289405248-0.1816492862661.76035142561-0.800829005906-0.4983488763191.90411126933-0.8892196164371.64546988094-17.9853206636-17.9101632197-56.1496348204
81.66417291004-2.11433337868-1.478657185272.681025275461.813825441631.307666165010.796384103870.202232011599-0.4301683239850.0899644737937-0.6983618817920.415275302463-0.9414634161980.125799140892-0.2356022971181.27044206826-0.7606734298060.2164038888851.75015479812-0.5760186359071.29385180999-21.0843234375-29.6289230934-49.285171293
90.5690780209490.435151470241-0.1359139754091.00639582530.08116961189891.41089334105-0.01487978534631.275404752890.537039754852-0.680550638311-0.4488059200640.750080425937-0.477289528424-0.7827802678420.2807873193130.7055915737520.199669851669-0.2940957980320.8534716296130.3603452381060.613529050812-16.763906253413.0117593382-27.9854197765
101.56591618111-0.643504398321-0.2473624709940.2747280978230.2175670716881.03597116979-0.5137533427651.25972283346-0.673562701614-0.2008051539880.02726868576670.277021547772-0.374832820559-0.6841969889040.5722303849371.27531749446-0.07321521262350.2512346425842.14209331834-0.4207890124550.86240784489-26.3884775171-10.5116177092-54.8797114738
110.431603440169-0.491451326499-0.7525287779393.4307747420.7574799458842.18089010161-0.4131044998541.326580032640.0446509060331-0.979478701910.3178817130131.15607326768-0.1886380654030.06191759039690.372240664040.675763797695-0.52657739249-0.2746236750982.77377476540.08082458950261.30407480221-31.8742191328-8.06842131446-49.5793429459
121.09808070435-0.6595351877410.1469741788031.00335256667-0.8060194288250.891510768352-0.5195189798420.6435814846290.360147389599-0.965864360778-0.4340274287440.824897705084-0.58621672782-0.02882392712840.5572032975831.17599437758-0.544171953815-0.5748891893032.18187907421-0.09578785908961.2267508897-30.8200117496-8.57740457881-53.2582201124
133.98265750633-1.20703723252.370348762875.05550681834-0.6462196270726.536925476480.180870391673-0.04375405709690.834279301074-0.37386745811-0.0771853992168-0.0980993462764-0.461158741639-0.1315128369090.0860619253780.2795684261930.164186561095-0.02655727927470.3955456984290.07513763328560.714718017261-11.130797155212.5743813907-8.24620061734
143.144562485660.823682941578-0.1512221297420.2255627887870.09494795204383.371411718920.213839765637-0.2636121736570.6303849724250.103329609869-0.07476022267650.339250168797-0.451641661334-0.438151783534-0.09078428764690.4442076931920.6881951925740.5487303789330.78883216171-0.07091071912140.505450666495-17.163302657815.04633994912.70827850271
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 47 )
2X-RAY DIFFRACTION2chain 'L' and (resid 48 through 101 )
3X-RAY DIFFRACTION3chain 'L' and (resid 102 through 130 )
4X-RAY DIFFRACTION4chain 'L' and (resid 131 through 143 )
5X-RAY DIFFRACTION5chain 'L' and (resid 144 through 163 )
6X-RAY DIFFRACTION6chain 'L' and (resid 164 through 173 )
7X-RAY DIFFRACTION7chain 'L' and (resid 174 through 185 )
8X-RAY DIFFRACTION8chain 'L' and (resid 186 through 205 )
9X-RAY DIFFRACTION9chain 'H' and (resid 1 through 119 )
10X-RAY DIFFRACTION10chain 'H' and (resid 120 through 142 )
11X-RAY DIFFRACTION11chain 'H' and (resid 143 through 173 )
12X-RAY DIFFRACTION12chain 'H' and (resid 174 through 222 )
13X-RAY DIFFRACTION13chain 'P' and (resid 658 through 667 )
14X-RAY DIFFRACTION14chain 'P' and (resid 668 through 677 )

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