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- EMDB-9401: CH505 SOSIP.664 trimer in complex with DH522.2 Fab -

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Basic information

Entry
Database: EMDB / ID: 9401
TitleCH505 SOSIP.664 trimer in complex with DH522.2 Fab
Map dataCH505 SOSIP.664 trimer in complex with DH522.2 Fab
SampleCH505 SOSIP.664 in complex with DH522.2 Fab:
CH505 SOSIP.664 / DH522.2 Fab / (nucleic-acidNucleic acid) x 3
SourceHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / 28.1 Å resolution
AuthorsFera D / Harrison SC
CitationJournal: Nat Commun / Year: 2017
Title: Initiation of HIV neutralizing B cell lineages with sequential envelope immunizations.
Authors: Wilton B Williams / Jinsong Zhang / Chuancang Jiang / Nathan I Nicely / Daniela Fera / Kan Luo / M Anthony Moody / Hua-Xin Liao / S Munir Alam / Thomas B Kepler / Akshaya Ramesh / Kevin Wiehe / James A Holland / Todd Bradley / Nathan Vandergrift / Kevin O Saunders / Robert Parks / Andrew Foulger / Shi-Mao Xia / Mattia Bonsignori / David C Montefiori / Mark Louder / Amanda Eaton / Sampa Santra / Richard Scearce / Laura Sutherland / Amanda Newman / Hilary Bouton-Verville / Cindy Bowman / Howard Bomze / Feng Gao / Dawn J Marshall / John F Whitesides / Xiaoyan Nie / Garnett Kelsoe / Steven G Reed / Christopher B Fox / Kim Clary / Marguerite Koutsoukos / David Franco / John R Mascola / Stephen C Harrison / Barton F Haynes / Laurent Verkoczy
DateDeposition: Sep 12, 2017 / Header (metadata) release: Oct 11, 2017 / Map release: Oct 11, 2017 / Last update: Dec 6, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.13
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.13
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9401.map.gz (map file in CCP4 format, 18967 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
168 pix
2.13 Å/pix.
= 357.84 Å
168 pix
2.13 Å/pix.
= 357.84 Å
168 pix
2.13 Å/pix.
= 357.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.13 Å
Density
Contour Level:2.13 (by author), 2.13 (movie #1):
Minimum - Maximum-17.361639 - 14.903893999999999
Average (Standard dev.)-0.0074381735 (0.9265896)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions168168168
Origin-84.0-84.0-84.0
Limit83.083.083.0
Spacing168168168
CellA=B=C: 357.84003 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.132.132.13
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z357.840357.840357.840
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-84-84-84
NC/NR/NS168168168
D min/max/mean-17.36214.904-0.007

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Supplemental data

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Sample components

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Entire CH505 SOSIP.664 in complex with DH522.2 Fab

EntireName: CH505 SOSIP.664 in complex with DH522.2 Fab / Number of components: 6

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Component #1: protein, CH505 SOSIP.664 in complex with DH522.2 Fab

ProteinName: CH505 SOSIP.664 in complex with DH522.2 Fab / Recombinant expression: No

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Component #2: protein, CH505 SOSIP.664

ProteinName: CH505 SOSIP.664 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, DH522.2 Fab

ProteinName: DH522.2 Fab / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: nucleic-acid, CH505 SOSIP.664

Nucleic-acidName: CH505 SOSIP.664 / Class: OTHER / Structure: OTHER / Synthetic: No
Sequence:
AENLWVTVYY GVPVWKEAKT TLFCASDAKA YEKEVHNVWA THACVPTDPN PQEMVLKNVT ENFNMWKNDM VDQMHEDVIS LWDQSLKPCV KLTPLCVTLN CTNATASNSS IIEGMKNCSF NITTELRDKR EKKNALFYKL DIVQLDGNSS QYRLINCNTS VITQACPKVS FDPIPIHYCA PAGYAILKCN NKTFTGTGPC NNVSTVQCTH GIKPVVSTQL LLNGSLAEGE IIIRSENITN NVKTIIVHLN ESVKIECTRP NNKTRTSIRI GPGQAFYATG QVIGDIREAY CNINESKWNE TLQRVSKKLK EYFPHKNITF QPSSGGDLEI TTHSFNCGGE FFYCNTSSLF NRTYMANSTD MANSTETNST RTITIHCRIK QIINMWQEVG RAMYAPPIAG NITCISNITG LLLTRDGGKN NTETFRPGGG NMKDNWRSEL YKYKVVKIEP LGVAPTRCKR RVVGRRRRRR AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSGK LICCTNVPWN SSWSNRNLSE IWDNMTWLQW DKEISNYTQI IYGLLEESQN QQEKNEQDLL ALD
SourceSpecies: Human immunodeficiency virus 1

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Component #5: nucleic-acid, DH522.2 Fab Heavy Chain

Nucleic-acidName: DH522.2 Fab Heavy Chain / Class: OTHER / Structure: OTHER / Synthetic: No
Sequence:
QVQLQESGPG LVKPSETLSL TCAVSGGSIG DDYYWNWIRQ SPGKGLEWIG SIYGSFGGTN FNPSLKNRVT ISMDTSNNQV SLKLNSVTAA DTAVYYCARG SHSIVVLFGY YFDYWGQGVL VTVSSASTKG PSVFPLAPSS RSTSESTAAL GCLVKDYFPE PVTVSWNSGS LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYVCNV NHKPSNTKVD KRVEIKT
SourceSpecies: Homo sapiens (human)

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Component #6: nucleic-acid, DH522.2 Fab Light Chain

Nucleic-acidName: DH522.2 Fab Light Chain / Class: OTHER / Structure: OTHER / Synthetic: No
Sequence:
QSALTQPPSV SKSLGQSVTI SCSGTTNDIG AYNGVSWYQH HSDTAPRLLI YEVNKRPSGV SDRFSGSKSG NTASLTISGL QAEDEADYYC GSYRSGSTWV FGGGTRLTVL GQPKASPTVT LFPPSSEELQ ANKATLVCLI SDFYPGVVKV AWKADGSAVN AGVETTTPSK QSNNKYAASS YLSLTSDQWK SHKSYSCQVT HEGSTVEKTV APAECS
SourceSpecies: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle
Sample solutionSpecimen conc.: 0.01 mg/ml / pH: 7.5
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 15269
3D reconstructionResolution: 28.1 Å / Resolution method: FSC 0.5 CUT-OFF

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