5UM8 | pdb_00005um8

Crystal structure of HIV-1 envelope trimer 16055 NFL TD CC (T569G) in complex with Fabs 35022 and PGT124


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.94 Å
  • R-Value Free: 
    0.329 (Depositor), 0.327 (DCC) 
  • R-Value Work: 
    0.260 (Depositor), 0.262 (DCC) 
  • R-Value Observed: 
    0.263 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Glycine Substitution at Helix-to-Coil Transitions Facilitates the Structural Determination of a Stabilized Subtype C HIV Envelope Glycoprotein.

Guenaga, J.Garces, F.de Val, N.Stanfield, R.L.Dubrovskaya, V.Higgins, B.Carrette, B.Ward, A.B.Wilson, I.A.Wyatt, R.T.

(2017) Immunity 46: 792-803.e3

  • DOI: https://doi.org/10.1016/j.immuni.2017.04.014
  • Primary Citation Related Structures: 
    5UM8

  • PubMed Abstract: 

    Advances in HIV-1 envelope glycoprotein (Env) design generate native-like trimers and high-resolution clade A, B, and G structures and elicit neutralizing antibodies. However, a high-resolution clade C structure is critical, as this subtype accounts for the majority of HIV infections worldwide, but well-ordered clade C Env trimers are more challenging to produce due to their instability. Based on targeted glycine substitutions in the Env fusion machinery, we defined a general approach that disfavors helical transitions leading to post-fusion conformations, thereby favoring the pre-fusion state. We generated a stabilized, soluble clade C Env (16055 NFL) and determined its crystal structure at 3.9 Å. Its overall conformation is similar to SOSIP.664 and native Env trimers but includes a covalent linker between gp120 and gp41, an engineered 201-433 disulfide bond, and density corresponding to 22 N-glycans. Env-structure-guided design strategies resulted in multiple homogeneous cross-clade immunogens with the potential to advance HIV vaccine development.


  • Organizational Affiliation
    • IAVI Neutralizing Antibody Center at The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 179.6 kDa 
  • Atom Count: 12,221 
  • Modeled Residue Count: 1,498 
  • Deposited Residue Count: 1,544 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
glycoprotein gp120A [auth G]485Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for A1EAI1 (Human immunodeficiency virus type 1)
Explore A1EAI1 
Go to UniProtKB:  A1EAI1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1EAI1
Glycosylation
Glycosylation Sites: 19
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
glycoprotein gp41153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for A1EAI1 (Human immunodeficiency virus type 1)
Explore A1EAI1 
Go to UniProtKB:  A1EAI1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1EAI1
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab PGT124 light chainC [auth L]214Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab PGT124 heavy chainD [auth H]236Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab 35022 heavy chainE [auth D]240Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab 35022 light chainF [auth E]216Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G [auth A],
H [auth C],
I [auth F],
J [auth I],
K [auth J],
G [auth A],
H [auth C],
I [auth F],
J [auth I],
K [auth J],
M,
O,
S
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseL [auth K]5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
N
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 10
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
P
10N-Glycosylation
Glycosylation Resources
GlyTouCan: G40702WU
GlyCosmos: G40702WU
GlyGen: G40702WU
Entity ID: 11
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Q
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G55220VL
GlyCosmos: G55220VL
GlyGen: G55220VL
Entity ID: 12
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
R
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G09724ZC
GlyCosmos: G09724ZC
GlyGen: G09724ZC

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
T [auth G]
U [auth G]
V [auth G]
AA [auth B],
BA [auth B],
T [auth G],
U [auth G],
V [auth G],
W [auth G],
X [auth G],
Y [auth G],
Z [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.94 Å
  • R-Value Free:  0.329 (Depositor), 0.327 (DCC) 
  • R-Value Work:  0.260 (Depositor), 0.262 (DCC) 
  • R-Value Observed: 0.263 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.456α = 90
b = 126.456β = 90
c = 314.093γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
International AIDS Vaccine InitativeUnited StatesOPP1084519
International AIDS Vaccine InitativeUnited StatesOPP1115782

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-06-21
    Changes: Source and taxonomy, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-10-30
    Changes: Structure summary